diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/basicPhysicalOperators.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/basicPhysicalOperators.scala
index b072a7f5d914..ca0cfb6834f1 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/basicPhysicalOperators.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/basicPhysicalOperators.scala
@@ -19,6 +19,7 @@ package org.apache.spark.sql.execution
 
 import java.util.concurrent.TimeUnit._
 
+import scala.collection.mutable
 import scala.concurrent.{ExecutionContext, Future}
 import scala.concurrent.duration.Duration
 
@@ -171,6 +172,7 @@ case class FilterExec(condition: Expression, child: SparkPlan)
     // This is very perf sensitive.
     // TODO: revisit this. We can consider reordering predicates as well.
     val generatedIsNotNullChecks = new Array[Boolean](notNullPreds.length)
+    val extraIsNotNullAttrs = mutable.Set[Attribute]()
     val generated = otherPreds.map { c =>
       val nullChecks = c.references.map { r =>
         val idx = notNullPreds.indexWhere { n => n.asInstanceOf[IsNotNull].child.semanticEquals(r)}
@@ -178,6 +180,9 @@ case class FilterExec(condition: Expression, child: SparkPlan)
           generatedIsNotNullChecks(idx) = true
           // Use the child's output. The nullability is what the child produced.
           genPredicate(notNullPreds(idx), input, child.output)
+        } else if (notNullAttributes.contains(r.exprId) && !extraIsNotNullAttrs.contains(r)) {
+          extraIsNotNullAttrs += r
+          genPredicate(IsNotNull(r), input, child.output)
         } else {
           ""
         }
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/SQLQuerySuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/SQLQuerySuite.scala
index b5d021549c7a..676e10fe59dc 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/SQLQuerySuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/SQLQuerySuite.scala
@@ -3233,6 +3233,32 @@ class SQLQuerySuite extends QueryTest with SharedSparkSession {
       }
     }
   }
+
+  test("SPARK-29213: FilterExec should not throw NPE") {
+    withTempView("t1", "t2", "t3") {
+      sql("SELECT ''").as[String].map(identity).toDF("x").createOrReplaceTempView("t1")
+      sql("SELECT * FROM VALUES 0, CAST(NULL AS BIGINT)")
+        .as[java.lang.Long]
+        .map(identity)
+        .toDF("x")
+        .createOrReplaceTempView("t2")
+      sql("SELECT ''").as[String].map(identity).toDF("x").createOrReplaceTempView("t3")
+      sql(
+        """
+          |SELECT t1.x
+          |FROM t1
+          |LEFT JOIN (
+          |    SELECT x FROM (
+          |        SELECT x FROM t2
+          |        UNION ALL
+          |        SELECT SUBSTR(x,5) x FROM t3
+          |    ) a
+          |    WHERE LENGTH(x)>0
+          |) t3
+          |ON t1.x=t3.x
+        """.stripMargin).collect()
+    }
+  }
 }
 
 case class Foo(bar: Option[String])