diff --git a/planner/core/exhaust_physical_plans.go b/planner/core/exhaust_physical_plans.go
index d9686dac8ebcd..dedf980ee063f 100644
--- a/planner/core/exhaust_physical_plans.go
+++ b/planner/core/exhaust_physical_plans.go
@@ -467,6 +467,11 @@ func (p *LogicalJoin) constructIndexJoin(
 				lhs, ok1 := c.GetArgs()[0].(*expression.Column)
 				rhs, ok2 := c.GetArgs()[1].(*expression.Column)
 				if ok1 && ok2 {
+					if lhs.InOperand || rhs.InOperand {
+						// if this other-cond is from a `[not] in` sub-query, do not convert it into eq-cond since
+						// IndexJoin cannot deal with NULL correctly in this case; please see #25799 for more details.
+						continue
+					}
 					outerSchema, innerSchema := p.Children()[outerIdx].Schema(), p.Children()[1-outerIdx].Schema()
 					if outerSchema.Contains(lhs) && innerSchema.Contains(rhs) {
 						outerHashKeys = append(outerHashKeys, lhs)
diff --git a/planner/core/integration_test.go b/planner/core/integration_test.go
index d33b1f5d31e11..55dbe6a33960b 100644
--- a/planner/core/integration_test.go
+++ b/planner/core/integration_test.go
@@ -3474,6 +3474,18 @@ func (s *testIntegrationSuite) TestIssue24281(c *C) {
 		"UNION select 1 as v1, 2 as v2")
 }
 
+func (s *testIntegrationSuite) TestIssue25799(c *C) {
+	tk := testkit.NewTestKit(c, s.store)
+	tk.MustExec("use test")
+	tk.MustExec("drop table if exists t1, t2")
+	tk.MustExec(`create table t1 (a float default null, b smallint(6) DEFAULT NULL)`)
+	tk.MustExec(`insert into t1 values (1, 1)`)
+	tk.MustExec(`create table t2 (a float default null, b tinyint(4) DEFAULT NULL, key b (b))`)
+	tk.MustExec(`insert into t2 values (null, 1)`)
+	tk.HasPlan(`select /*+ TIDB_INLJ(t2@sel_2) */ t1.a, t1.b from t1 where t1.a not in (select t2.a from t2 where t1.b=t2.b)`, `IndexJoin`)
+	tk.MustQuery(`select /*+ TIDB_INLJ(t2@sel_2) */ t1.a, t1.b from t1 where t1.a not in (select t2.a from t2 where t1.b=t2.b)`).Check(testkit.Rows())
+}
+
 func (s *testIntegrationSuite) TestLimitWindowColPrune(c *C) {
 	tk := testkit.NewTestKit(c, s.store)
 	tk.MustExec("use test")