diff --git a/src/learner.cc b/src/learner.cc
index a7bd47e65283..7d8419259e1e 100644
--- a/src/learner.cc
+++ b/src/learner.cc
@@ -397,7 +397,7 @@ class LearnerConfiguration : public Learner {
       this->ValidateParameters();
     }
 
-    // FIXME(trivialfis): Clear the cache once binary IO is gone.
+    cfg_.clear();
     monitor_.Stop("Configure");
   }