diff --git a/.changeset/popular-colts-visit.md b/.changeset/popular-colts-visit.md
new file mode 100644
index 0000000000..30fffa29a0
--- /dev/null
+++ b/.changeset/popular-colts-visit.md
@@ -0,0 +1,5 @@
+---
+'@backstage/core-components': patch
+---
+
+Deprecated CheckboxTree component. Deprecated the filter type `'checkbox-tree'` from the `TableFilter` types.
diff --git a/packages/core-components/api-report.md b/packages/core-components/api-report.md
index f4539faae0..e987d6b67e 100644
--- a/packages/core-components/api-report.md
+++ b/packages/core-components/api-report.md
@@ -1889,7 +1889,7 @@ export interface TableColumn<T extends object = {}> extends Column<T> {
 // @public (undocumented)
 export type TableFilter = {
   column: string;
-  type: 'select' | 'multiple-select' | 'checkbox-tree';
+  type: 'select' | 'multiple-select' | /** @deprecated */ 'checkbox-tree';
 };
 
 // Warning: (ae-missing-release-tag) "TableProps" is exported by the package, but it is missing a release tag (@alpha, @beta, @public, or @internal)
diff --git a/packages/core-components/src/components/CheckboxTree/CheckboxTree.tsx b/packages/core-components/src/components/CheckboxTree/CheckboxTree.tsx
index 695da88192..71b5cf7659 100644
--- a/packages/core-components/src/components/CheckboxTree/CheckboxTree.tsx
+++ b/packages/core-components/src/components/CheckboxTree/CheckboxTree.tsx
@@ -225,6 +225,10 @@ const indexer = (
     };
   }, {});
 
+/**
+ *
+ * @deprecated CheckboxTree is no longer used in Table filters
+ */
 export function CheckboxTree(props: CheckboxTreeProps) {
   const { subCategories, label, selected, onChange, triggerReset } = props;
   const classes = useStyles();
diff --git a/packages/core-components/src/components/Table/Filters.tsx b/packages/core-components/src/components/Table/Filters.tsx
index 5e2611fba4..b482e6c808 100644
--- a/packages/core-components/src/components/Table/Filters.tsx
+++ b/packages/core-components/src/components/Table/Filters.tsx
@@ -53,7 +53,7 @@ const useSubvalueCellStyles = makeStyles<BackstageTheme>(theme => ({
 export type Without<T, K> = Pick<T, Exclude<keyof T, K>>;
 
 export type Filter = {
-  type: 'select' | 'checkbox-tree' | 'multiple-select';
+  type: 'select' | /** @deprecated */ 'checkbox-tree' | 'multiple-select';
   element:
     | Without<CheckboxTreeProps, 'onChange'>
     | Without<SelectProps, 'onChange'>;
diff --git a/packages/core-components/src/components/Table/Table.tsx b/packages/core-components/src/components/Table/Table.tsx
index edc5fd33ce..ecde7e992b 100644
--- a/packages/core-components/src/components/Table/Table.tsx
+++ b/packages/core-components/src/components/Table/Table.tsx
@@ -191,7 +191,7 @@ export interface TableColumn<T extends object = {}> extends Column<T> {
 
 export type TableFilter = {
   column: string;
-  type: 'select' | 'multiple-select' | 'checkbox-tree';
+  type: 'select' | 'multiple-select' | /** @deprecated */ 'checkbox-tree';
 };
 
 export type TableState = {
@@ -365,6 +365,14 @@ export function Table<T extends object = {}>(props: TableProps<T>) {
     setSelectedFiltersLength(selectedFiltersArray.flat().length);
   }, [data, selectedFilters, getFieldByTitle]);
 
+  // Check for deprecated checkbox-tree filter
+  useEffect(() => {
+    if (filters?.some(filter => filter.type === 'checkbox-tree')) {
+      // eslint-disable-next-line no-console
+      console.warn('"checkbox-tree" filter type is deprecated');
+    }
+  }, [filters]);
+
   const constructFilters = (
     filterConfig: TableFilter[],
     dataValue: any[] | undefined,