diff --git a/src/learner.cc b/src/learner.cc
index 6a95e0bab..a88f967c4 100644
--- a/src/learner.cc
+++ b/src/learner.cc
@@ -189,10 +189,10 @@ class LearnerImpl : public Learner {
       mparam.InitAllowUnknown(args);
       name_obj_ = cfg_["objective"];
       name_gbm_ = cfg_["booster"];
+      // set seed only before the model is initialized
+      common::GlobalRandom().seed(tparam.seed);
     }
 
-    common::GlobalRandom().seed(tparam.seed);
-
     // set number of features correctly.
     cfg_["num_feature"] = common::ToString(mparam.num_feature);
     cfg_["num_class"] = common::ToString(mparam.num_class);