diff --git a/doc/whatsnew/fragments/10969.bugfix b/doc/whatsnew/fragments/10969.bugfix
new file mode 100644
index 0000000000..e8584fb235
--- /dev/null
+++ b/doc/whatsnew/fragments/10969.bugfix
@@ -0,0 +1,7 @@
+Fix an issue where discovery can miss a similarly named directory if a shorter named directory is processed first.
+
+If you have directories named say `applications` and `applications_api` in a
+project, and the former is encountered by the tree walk first during discovery,
+the second directory would be skipped even if it was a valid package. This fixes
+the issue by appending the OS filepath separator to the name in the case where
+the path was known to be a directory due to having an `__init__.py` in it.
diff --git a/pylint/lint/pylinter.py b/pylint/lint/pylinter.py
index d3399ecba4..101cbbcdd2 100644
--- a/pylint/lint/pylinter.py
+++ b/pylint/lint/pylinter.py
@@ -685,7 +685,7 @@ def _discover_files(self, files_or_modules: Sequence[str]) -> Iterator[str]:
                         continue
 
                     if "__init__.py" in files:
-                        skip_subtrees.append(root)
+                        skip_subtrees.append(root + os.sep)
                         yield root
                     else:
                         yield from (