diff --git a/frontend/src/pages/LinkMLViewerPage.tsx b/frontend/src/pages/LinkMLViewerPage.tsx
index 1ba6b5135a..e17a948d3f 100644
--- a/frontend/src/pages/LinkMLViewerPage.tsx
+++ b/frontend/src/pages/LinkMLViewerPage.tsx
@@ -1691,6 +1691,8 @@ const LinkMLViewerPage: React.FC = () => {
   const navigateToClass = useCallback((className: string) => {
     setSearchParams({ class: className });
     setHighlightedClass(className);
+    // Close any open ontology popup when navigating
+    setOntologyPopupCurie(null);
     
     // Find and select the class file
     const classFile = categories
@@ -1708,6 +1710,8 @@ const LinkMLViewerPage: React.FC = () => {
   const navigateToEnum = useCallback((enumName: string) => {
     setSearchParams({ enum: enumName });
     setHighlightedClass(enumName);  // Reuse highlight state for enums
+    // Close any open ontology popup when navigating
+    setOntologyPopupCurie(null);
     
     // Find and select the enum file
     const enumFile = categories
@@ -1725,6 +1729,8 @@ const LinkMLViewerPage: React.FC = () => {
   const navigateToSlot = useCallback((slotName: string) => {
     setSearchParams({ slot: slotName });
     setHighlightedClass(slotName);  // Reuse highlight state for slots
+    // Close any open ontology popup when navigating
+    setOntologyPopupCurie(null);
     
     // Find and select the slot file
     const slotFile = categories
@@ -3654,8 +3660,9 @@ const LinkMLViewerPage: React.FC = () => {
                           } else if (category.name === 'slot') {
                             navigateToSlot(file.name);
                           } else {
-                            // For main schemas, clear the deep link params
+                            // For main schemas, clear the deep link params and close any popup
                             setSearchParams({});
+                            setOntologyPopupCurie(null);
                           }
                         }}
                       >