diff --git a/docs/inputs.rst b/docs/inputs.rst
index d87acd2203..3a3c7f14bb 100644
--- a/docs/inputs.rst
+++ b/docs/inputs.rst
@@ -19,6 +19,11 @@ JSON format).
 When uploading through the Web UI, navigate to your project and use the upload
 interface in the "Inputs" panel.
 
+.. note::
+
+    Uploading directories or folders directly is not supported. Please compress
+    directories into an archive (such as ``.zip`` or ``.tar.gz``) before uploading.
+
 For REST API uploads, refer to the :ref:`rest_api` documentation for endpoint details.
 
 .. _inputs_download_url:
diff --git a/scancodeio/static/js/add_inputs.js b/scancodeio/static/js/add_inputs.js
index 1850759c38..b0a79489dc 100644
--- a/scancodeio/static/js/add_inputs.js
+++ b/scancodeio/static/js/add_inputs.js
@@ -22,11 +22,14 @@
 
 const fileInput = document.querySelector("#id_input_files");
 let selectedFiles = []; // Store selected files
-fileInput.onchange = updateFiles;
+let folderAlertTimeout = null;
+if (fileInput) {
+  fileInput.onchange = updateFiles;
+}
 
 // Update the list of files to be uploaded in the UI
 function updateFiles() {
-  if (fileInput.files.length > 0) {
+  if (fileInput && fileInput.files.length > 0) {
     const fileName = document.querySelector("#inputs_file_name");
     fileName.replaceChildren();
 
@@ -100,24 +103,206 @@ function removeFile(fileName) {
     dataTransfer.items.add(file);
   }
 
-  fileInput.files = dataTransfer.files;
+  if (fileInput) {
+    fileInput.files = dataTransfer.files;
+  }
+}
+
+function inspectDataTransfer(dataTransfer) {
+  const validFiles = [];
+  const rejectedFolders = [];
+
+  const items = dataTransfer.items;
+  if (items && items.length > 0) {
+    for (let i = 0; i < items.length; i++) {
+      const item = items[i];
+      if (item.kind !== "file") continue;
+
+      const entry = item.webkitGetAsEntry ? item.webkitGetAsEntry() : null;
+      if (entry) {
+        if (entry.isDirectory) {
+          rejectedFolders.push(entry.name || "folder");
+          continue;
+        }
+      }
+
+      const file = item.getAsFile ? item.getAsFile() : null;
+      if (file) {
+        validFiles.push(file);
+      }
+    }
+  } else if (dataTransfer.files && dataTransfer.files.length > 0) {
+    for (const file of dataTransfer.files) {
+      validFiles.push(file);
+    }
+  }
+
+  return { validFiles, rejectedFolders };
+}
+
+function showFolderUploadWarning(count) {
+  const inputFilesBox = document.querySelector("#input_files_box");
+  if (!inputFilesBox) return;
+
+  const fileCta = inputFilesBox.querySelector(".file-cta");
+  if (fileCta) {
+    fileCta.classList.remove("has-folder-error");
+    void fileCta.offsetWidth;
+    fileCta.classList.add("has-folder-error");
+    setTimeout(() => {
+      fileCta.classList.remove("has-folder-error");
+    }, 600);
+  }
+
+  if (folderAlertTimeout) {
+    clearTimeout(folderAlertTimeout);
+    folderAlertTimeout = null;
+  }
+
+  let tray = inputFilesBox.querySelector(".folder-notice-tray");
+  let isNew = false;
+
+  if (!tray) {
+    isNew = true;
+    tray = document.createElement("div");
+    tray.className = "folder-notice-tray";
+    tray.setAttribute("role", "alert");
+    tray.setAttribute("aria-live", "polite");
+
+    const inner = document.createElement("div");
+    inner.className = "folder-notice-inner";
+
+    const bar = document.createElement("div");
+    bar.className = "folder-notice-bar";
+
+    const main = document.createElement("div");
+    main.className = "folder-notice-main";
+
+    const iconSpan = document.createElement("span");
+    iconSpan.className = "folder-notice-icon";
+    const icon = document.createElement("i");
+    icon.className = "fa-solid fa-folder-minus";
+    iconSpan.appendChild(icon);
+    main.appendChild(iconSpan);
+
+    const msg = document.createElement("span");
+    msg.className = "folder-notice-msg";
+    msg.append("Folders cannot be uploaded directly. Please upload a ");
+
+    const zipKbd = document.createElement("kbd");
+    zipKbd.className = "folder-notice-kbd";
+    zipKbd.textContent = ".zip";
+    msg.appendChild(zipKbd);
+
+    msg.append(" or ");
+
+    const tarKbd = document.createElement("kbd");
+    tarKbd.className = "folder-notice-kbd";
+    tarKbd.textContent = ".tar.gz";
+    msg.appendChild(tarKbd);
+
+    msg.append(" archive instead.");
+
+    const countSpan = document.createElement("span");
+    countSpan.className = "folder-notice-count";
+    countSpan.textContent = `(Folders skipped: ${count || 1})`;
+    msg.appendChild(countSpan);
+
+    main.appendChild(msg);
+
+    const dismissBtn = document.createElement("button");
+    dismissBtn.type = "button";
+    dismissBtn.className = "folder-notice-dismiss";
+    dismissBtn.setAttribute("aria-label", "Dismiss notice");
+    dismissBtn.setAttribute("title", "Dismiss");
+    const dismissIcon = document.createElement("i");
+    dismissIcon.className = "fa-solid fa-xmark";
+    dismissBtn.appendChild(dismissIcon);
+
+    bar.appendChild(main);
+    bar.appendChild(dismissBtn);
+    inner.appendChild(bar);
+    tray.appendChild(inner);
+
+    inputFilesBox.appendChild(tray);
+    inputFilesBox.classList.add("has-folder-notice");
+  } else {
+    const countSpan = tray.querySelector(".folder-notice-count");
+    if (countSpan && count) {
+      countSpan.textContent = `(Folders skipped: ${count})`;
+    }
+  }
+
+  function dismiss() {
+    if (folderAlertTimeout) {
+      clearTimeout(folderAlertTimeout);
+      folderAlertTimeout = null;
+    }
+    if (tray && tray.parentNode) {
+      tray.classList.remove("is-open");
+      setTimeout(() => {
+        if (tray && tray.parentNode) {
+          tray.remove();
+        }
+        if (inputFilesBox && !inputFilesBox.querySelector(".folder-notice-tray")) {
+          inputFilesBox.classList.remove("has-folder-notice");
+        }
+      }, 230);
+    }
+  }
+
+  const dismissBtn = tray.querySelector(".folder-notice-dismiss");
+  if (dismissBtn) {
+    dismissBtn.onclick = dismiss;
+  }
+
+  if (isNew) {
+    requestAnimationFrame(() => {
+      requestAnimationFrame(() => {
+        tray.classList.add("is-open");
+      });
+    });
+  }
+
+  folderAlertTimeout = setTimeout(dismiss, 8000);
+  tray.onmouseenter = () => {
+    if (folderAlertTimeout) {
+      clearTimeout(folderAlertTimeout);
+      folderAlertTimeout = null;
+    }
+  };
+  tray.onmouseleave = () => {
+    folderAlertTimeout = setTimeout(dismiss, 3000);
+  };
 }
 
 function dropHandler(event) {
   disableEvent(event);
 
-  // Merge existing files and dropped files, let updateFiles handle dedup
-  const dataTransfer = new DataTransfer();
-  for (const file of [...fileInput.files, ...event.dataTransfer.files]) {
-    dataTransfer.items.add(file);
+  const { validFiles, rejectedFolders } = inspectDataTransfer(event.dataTransfer);
+
+  if (rejectedFolders.length > 0) {
+    showFolderUploadWarning(rejectedFolders.length);
   }
 
-  fileInput.files = dataTransfer.files;
-  updateFiles();
+  if (validFiles.length > 0) {
+    const dataTransfer = new DataTransfer();
+    const existing = fileInput ? fileInput.files : [];
+    for (const file of [...existing, ...validFiles]) {
+      dataTransfer.items.add(file);
+    }
+
+    if (fileInput) {
+      fileInput.files = dataTransfer.files;
+      updateFiles();
+    }
+  }
 }
 
 // Handle drag and drop events
 const inputFilesBox = document.querySelector("#input_files_box");
-inputFilesBox.addEventListener("dragenter", disableEvent);
-inputFilesBox.addEventListener("dragover", disableEvent);
-inputFilesBox.addEventListener("drop", dropHandler);
+if (inputFilesBox) {
+  inputFilesBox.addEventListener("dragenter", disableEvent);
+  inputFilesBox.addEventListener("dragover", disableEvent);
+  inputFilesBox.addEventListener("drop", dropHandler);
+}
diff --git a/scancodeio/static/main.css b/scancodeio/static/main.css
index f85577d7d1..0c302166d5 100644
--- a/scancodeio/static/main.css
+++ b/scancodeio/static/main.css
@@ -327,9 +327,218 @@ button.as-link {
 .input.is-smaller {
   font-size: 0.9rem;
 }
+:root {
+  --folder-notice-bg: #fffdf7;
+  --folder-notice-border: #fcd34d;
+  --folder-notice-divider: rgba(217, 119, 6, 0.2);
+  --folder-notice-accent: #d97706;
+  --folder-notice-text: #78350f;
+  --folder-notice-kbd-bg: rgba(217, 119, 6, 0.08);
+  --folder-notice-kbd-border: rgba(217, 119, 6, 0.22);
+  --folder-notice-kbd-text: #92400e;
+  --folder-notice-hover: rgba(120, 53, 15, 0.08);
+  --folder-notice-glow: rgba(217, 119, 6, 0.18);
+  --folder-notice-cta-tint: rgba(245, 158, 11, 0.04);
+}
+
+@media (prefers-color-scheme: dark) {
+  :root:not([data-theme="light"]) {
+    --folder-notice-bg: #1c1f26;
+    --folder-notice-border: #374151;
+    --folder-notice-divider: rgba(245, 158, 11, 0.25);
+    --folder-notice-accent: #fbbf24;
+    --folder-notice-text: #f3f4f6;
+    --folder-notice-kbd-bg: rgba(255, 255, 255, 0.08);
+    --folder-notice-kbd-border: rgba(255, 255, 255, 0.16);
+    --folder-notice-kbd-text: #fde68a;
+    --folder-notice-hover: rgba(255, 255, 255, 0.1);
+    --folder-notice-glow: rgba(245, 158, 11, 0.2);
+    --folder-notice-cta-tint: rgba(245, 158, 11, 0.06);
+  }
+}
+
+[data-theme="dark"],
+.theme-dark {
+  --folder-notice-bg: #1c1f26;
+  --folder-notice-border: #374151;
+  --folder-notice-divider: rgba(245, 158, 11, 0.25);
+  --folder-notice-accent: #fbbf24;
+  --folder-notice-text: #f3f4f6;
+  --folder-notice-kbd-bg: rgba(255, 255, 255, 0.08);
+  --folder-notice-kbd-border: rgba(255, 255, 255, 0.16);
+  --folder-notice-kbd-text: #fde68a;
+  --folder-notice-hover: rgba(255, 255, 255, 0.1);
+  --folder-notice-glow: rgba(245, 158, 11, 0.2);
+  --folder-notice-cta-tint: rgba(245, 158, 11, 0.06);
+}
+
+[data-theme="light"],
+.theme-light {
+  --folder-notice-bg: #fffdf7;
+  --folder-notice-border: #fcd34d;
+  --folder-notice-divider: rgba(217, 119, 6, 0.2);
+  --folder-notice-accent: #d97706;
+  --folder-notice-text: #78350f;
+  --folder-notice-kbd-bg: rgba(217, 119, 6, 0.08);
+  --folder-notice-kbd-border: rgba(217, 119, 6, 0.22);
+  --folder-notice-kbd-text: #92400e;
+  --folder-notice-hover: rgba(120, 53, 15, 0.08);
+  --folder-notice-glow: rgba(217, 119, 6, 0.18);
+  --folder-notice-cta-tint: rgba(245, 158, 11, 0.04);
+}
+
+#input_files_box {
+  flex-direction: column;
+}
+
 .file.is-boxed.has-name .file-cta {
   border-width: medium;
   border-style: dashed;
+  transition: border-color 220ms cubic-bezier(0.25, 1, 0.5, 1),
+              background-color 220ms cubic-bezier(0.25, 1, 0.5, 1),
+              box-shadow 220ms cubic-bezier(0.25, 1, 0.5, 1);
+}
+
+.file.is-boxed.has-name .file-cta.has-folder-error {
+  border-color: var(--folder-notice-accent) !important;
+  background-color: var(--folder-notice-cta-tint) !important;
+  box-shadow: 0 0 0 3px var(--folder-notice-glow) !important;
+}
+
+#input_files_box.has-folder-notice #inputs_file_name {
+  border-bottom-left-radius: 0 !important;
+  border-bottom-right-radius: 0 !important;
+  border-bottom-color: var(--folder-notice-divider) !important;
+  transition: border-radius 220ms cubic-bezier(0.25, 1, 0.5, 1),
+              border-bottom-color 220ms ease;
+}
+
+.folder-notice-tray {
+  display: grid;
+  grid-template-rows: 0fr;
+  opacity: 0;
+  width: 100%;
+  transition: grid-template-rows 220ms cubic-bezier(0.25, 1, 0.5, 1),
+              opacity 180ms ease;
+  will-change: grid-template-rows, opacity;
+}
+
+.folder-notice-tray.is-open {
+  grid-template-rows: 1fr;
+  opacity: 1;
+  transition: grid-template-rows 280ms cubic-bezier(0.16, 1, 0.3, 1),
+              opacity 200ms ease;
+}
+
+.folder-notice-inner {
+  overflow: hidden;
+  min-height: 0;
+}
+
+.folder-notice-bar {
+  display: flex;
+  align-items: flex-start;
+  justify-content: space-between;
+  gap: 0.85rem;
+  padding: 0.55rem 0.85rem;
+  font-size: 0.8125rem;
+  line-height: 1.45;
+  background-color: var(--folder-notice-bg);
+  border: 1px solid var(--folder-notice-border);
+  border-top: none;
+  border-bottom-left-radius: var(--bulma-file-radius, var(--bulma-radius, 6px));
+  border-bottom-right-radius: var(--bulma-file-radius, var(--bulma-radius, 6px));
+  color: var(--folder-notice-text);
+  box-shadow: inset 0 1px 0 var(--folder-notice-divider);
+}
+
+.folder-notice-main {
+  display: flex;
+  align-items: flex-start;
+  gap: 0.75rem;
+  flex: 1;
+  min-width: 0;
+}
+
+.folder-notice-icon {
+  flex-shrink: 0;
+  display: inline-flex;
+  align-items: center;
+  justify-content: center;
+  color: var(--folder-notice-accent);
+  font-size: 0.95rem;
+  line-height: 1;
+  margin-top: 0.125rem;
+}
+
+.folder-notice-msg {
+  color: var(--folder-notice-text);
+}
+
+.folder-notice-msg strong {
+  color: inherit;
+  font-weight: 600;
+}
+
+.folder-notice-kbd {
+  display: inline-block;
+  padding: 0.08em 0.35em;
+  font-family: var(--bulma-family-monospace, monospace);
+  font-size: 0.75rem;
+  font-weight: 600;
+  line-height: 1.2;
+  border-radius: 3px;
+  background-color: var(--folder-notice-kbd-bg);
+  border: 1px solid var(--folder-notice-kbd-border);
+  color: var(--folder-notice-kbd-text);
+  vertical-align: baseline;
+}
+
+.folder-notice-count {
+  display: inline-block;
+  margin-left: 0.4rem;
+  font-size: 0.775rem;
+  opacity: 0.85;
+  white-space: nowrap;
+}
+
+.folder-notice-dismiss {
+  flex-shrink: 0;
+  display: inline-flex;
+  align-items: center;
+  justify-content: center;
+  width: 1.35rem;
+  height: 1.35rem;
+  padding: 0;
+  border: none;
+  background: transparent;
+  color: var(--folder-notice-text);
+  opacity: 0.6;
+  border-radius: 4px;
+  cursor: pointer;
+  font-size: 0.875rem;
+  line-height: 1;
+  margin-top: -0.05rem;
+  transition: opacity 140ms ease, background-color 140ms ease, transform 80ms ease;
+}
+
+.folder-notice-dismiss:hover {
+  opacity: 1;
+  background-color: var(--folder-notice-hover);
+}
+
+.folder-notice-dismiss:active {
+  transform: scale(0.9);
+}
+
+@media (prefers-reduced-motion: reduce) {
+  .folder-notice-tray,
+  .folder-notice-bar,
+  .file.is-boxed.has-name .file-cta,
+  #input_files_box.has-folder-notice #inputs_file_name {
+    transition: none !important;
+    transform: none !important;
+  }
 }
 progress.file-upload::before {
   content: "Files upload: " attr(value) "%";