diff --git a/src/components/file-tree/hooks/useFileTreeUpload.ts b/src/components/file-tree/hooks/useFileTreeUpload.ts
index 37cd936dcb..ac90f586c9 100644
--- a/src/components/file-tree/hooks/useFileTreeUpload.ts
+++ b/src/components/file-tree/hooks/useFileTreeUpload.ts
@@ -374,9 +374,17 @@ export const useFileTreeUpload = ({
     ],
   );
 
+  /**
+   * Upload the picked files into the given target folder.
+   *
+   * @param fileList   Files chosen via the File Explorer input or drop.
+   * @param targetPath Project-relative folder to upload into; defaults to ''
+   *                   (the project root). Validated server-side via
+   *                   validatePathInProject.
+   */
   const handleFileSelect = useCallback(
-    async (fileList: FileList | File[]) => {
-      await uploadFiles(Array.from(fileList), '');
+    async (fileList: FileList | File[], targetPath = '') => {
+      await uploadFiles(Array.from(fileList), targetPath);
     },
     [uploadFiles],
   );
diff --git a/src/components/file-tree/view/FileTree.tsx b/src/components/file-tree/view/FileTree.tsx
index bd90c36b33..dba5f95bcf 100644
--- a/src/components/file-tree/view/FileTree.tsx
+++ b/src/components/file-tree/view/FileTree.tsx
@@ -92,10 +92,20 @@ export default function FileTree({ selectedProject, onFileOpen }: FileTreeProps)
     return <Icon className={cn(ICON_SIZE_CLASS, color)} />;
   }, []);
 
-  // Centralized click behavior keeps file actions identical across all presentation modes.
+  const [selectedUploadDir, setSelectedUploadDir] = useState<string>('');
+
+  /**
+   * Centralized click behavior keeps file actions identical across all
+   * presentation modes. Clicking a directory also marks it as the upload
+   * target, so subsequent File Explorer uploads land in that folder instead
+   * of the project root.
+   *
+   * @param item The file-tree node that was clicked.
+   */
   const handleItemClick = useCallback(
     (item: FileTreeNode) => {
       if (item.type === 'directory') {
+        setSelectedUploadDir(item.path);
         toggleDirectory(item.path);
         return;
       }
@@ -150,7 +160,7 @@ export default function FileTree({ selectedProject, onFileOpen }: FileTreeProps)
         onViewModeChange={changeViewMode}
         searchQuery={searchQuery}
         onSearchQueryChange={setSearchQuery}
-        onUploadFiles={upload.handleFileSelect}
+        onUploadFiles={(files) => upload.handleFileSelect(files, selectedUploadDir)}
         onNewFile={() => operations.handleStartCreate('', 'file')}
         onNewFolder={() => operations.handleStartCreate('', 'directory')}
         onRefresh={refreshFiles}
@@ -161,6 +171,23 @@ export default function FileTree({ selectedProject, onFileOpen }: FileTreeProps)
         uploadProgress={upload.uploadProgress?.progress ?? null}
       />
 
+      {selectedUploadDir && (
+        <div className="flex items-center gap-1.5 px-3 py-0.5 text-xs text-muted-foreground">
+          <span className="truncate">
+            {t('fileTree.uploadTarget', 'Upload target')}: {selectedUploadDir}
+          </span>
+          <button
+            type="button"
+            onClick={() => setSelectedUploadDir('')}
+            className="shrink-0 rounded p-0.5 hover:text-foreground"
+            title={t('fileTree.uploadTargetReset', 'Reset upload target to project root')}
+            aria-label={t('fileTree.uploadTargetReset', 'Reset upload target to project root')}
+          >
+            <X className="h-3 w-3" />
+          </button>
+        </div>
+      )}
+
       <FileTreeUploadProgress upload={upload.uploadProgress} />
 
       {viewMode === 'detailed' && filteredFiles.length > 0 && <FileTreeDetailedColumns />}