diff --git a/sessionctx/variable/session_test.go b/sessionctx/variable/session_test.go
index 6d461f772c..708b963958 100644
--- a/sessionctx/variable/session_test.go
+++ b/sessionctx/variable/session_test.go
@@ -15,6 +15,7 @@
 package variable_test
 
 import (
+	"sync"
 	"testing"
 	"time"
 
@@ -34,6 +35,7 @@ func TestSetSystemVariable(t *testing.T) {
 	v := variable.NewSessionVars()
 	v.GlobalVarsAccessor = variable.NewMockGlobalAccessor()
 	v.TimeZone = time.UTC
+	mtx := new(sync.Mutex)
 
 	testCases := []struct {
 		key   string
@@ -57,7 +59,10 @@ func TestSetSystemVariable(t *testing.T) {
 
 	for _, tc := range testCases {
 		t.Run(tc.key, func(t *testing.T) {
+			t.Parallel()
+			mtx.Lock()
 			err := variable.SetSessionSystemVar(v, tc.key, tc.value)
+			mtx.Unlock()
 			if tc.err {
 				require.Error(t, err)
 			} else {
diff --git a/sessionctx/variable/sysvar.go b/sessionctx/variable/sysvar.go
index 4a972b830a..75f4cc1695 100644
--- a/sessionctx/variable/sysvar.go
+++ b/sessionctx/variable/sysvar.go
@@ -1269,7 +1269,7 @@ var defaultSysVars = []*SysVar{
 		s.EnableFastAnalyze = TiDBOptOn(val)
 		return nil
 	}},
-	{Scope: ScopeGlobal | ScopeSession, Name: TiDBSkipIsolationLevelCheck, skipInit: true, Value: BoolToOnOff(DefTiDBSkipIsolationLevelCheck), Type: TypeBool},
+	{Scope: ScopeGlobal | ScopeSession, Name: TiDBSkipIsolationLevelCheck, Value: BoolToOnOff(DefTiDBSkipIsolationLevelCheck), Type: TypeBool},
 	{Scope: ScopeGlobal | ScopeSession, Name: TiDBEnableRateLimitAction, Value: BoolToOnOff(DefTiDBEnableRateLimitAction), Type: TypeBool, SetSession: func(s *SessionVars, val string) error {
 		s.EnabledRateLimitAction = TiDBOptOn(val)
 		return nil
diff --git a/sessionctx/variable/sysvar_test.go b/sessionctx/variable/sysvar_test.go
index 78793a1725..257e3beec8 100644
--- a/sessionctx/variable/sysvar_test.go
+++ b/sessionctx/variable/sysvar_test.go
@@ -419,8 +419,21 @@ func TestTxnIsolation(t *testing.T) {
 	_, err = sv.Validate(vars, "read-uncommitted", ScopeSession)
 	require.Equal(t, "[variable:8048]The isolation level 'READ-UNCOMMITTED' is not supported. Set tidb_skip_isolation_level_check=1 to skip this error", err.Error())
 
-	vars.systems[TiDBSkipIsolationLevelCheck] = "ON"
+	// Enable global skip isolation check doesn't affect current session
+	require.Nil(t, GetSysVar(TiDBSkipIsolationLevelCheck).SetGlobalFromHook(vars, "ON", true))
+	_, err = sv.Validate(vars, "Serializable", ScopeSession)
+	require.Equal(t, "[variable:8048]The isolation level 'SERIALIZABLE' is not supported. Set tidb_skip_isolation_level_check=1 to skip this error", err.Error())
 
+	// Enable session skip isolation check
+	require.Nil(t, GetSysVar(TiDBSkipIsolationLevelCheck).SetSessionFromHook(vars, "ON"))
+
+	val, err = sv.Validate(vars, "Serializable", ScopeSession)
+	require.NoError(t, err)
+	require.Equal(t, "SERIALIZABLE", val)
+
+	// Init TiDBSkipIsolationLevelCheck like what loadCommonGlobalVariables does
+	vars = NewSessionVars()
+	require.NoError(t, vars.SetSystemVarWithRelaxedValidation(TiDBSkipIsolationLevelCheck, "1"))
 	val, err = sv.Validate(vars, "Serializable", ScopeSession)
 	require.NoError(t, err)
 	require.Equal(t, "SERIALIZABLE", val)