diff --git a/CPPLINT.cfg b/CPPLINT.cfg
index 27c1bfc6148a..6ee23ad759a1 100644
--- a/CPPLINT.cfg
+++ b/CPPLINT.cfg
@@ -20,6 +20,12 @@ filter=+build/pragma_once
 # Disable cpplint's include order.  We have our own via //tools:drakelint.
 filter=-build/include_order
 
+# Disable cpplint's check to include the h file atop the cc file (along with
+# some other, even less relevant checks). Given the layout of bazel's runfiles
+# during linting and our include path customizations, cpplint yields false
+# positives because it's unable to discern the root of our include path.
+filter=-build/include
+
 # We do not care about the whitespace details of a TODO comment.  It is not
 # relevant for easy grepping, and the GSG does not specify any particular
 # whitespace style.  (We *do* care what the "TODO(username)" itself looks like