diff --git a/cmd/pipecd/BUILD.bazel b/cmd/pipecd/BUILD.bazel
index 5c8368b9b4..213427af08 100644
--- a/cmd/pipecd/BUILD.bazel
+++ b/cmd/pipecd/BUILD.bazel
@@ -22,6 +22,7 @@ go_library(
         "//pkg/app/api/stagelogstore:go_default_library",
         "//pkg/app/ops/handler:go_default_library",
         "//pkg/app/ops/insightcollector:go_default_library",
+        "//pkg/app/ops/orphancommandcleaner:go_default_library",
         "//pkg/backoff:go_default_library",
         "//pkg/cache/rediscache:go_default_library",
         "//pkg/cli:go_default_library",
diff --git a/cmd/pipecd/ops.go b/cmd/pipecd/ops.go
index 4e341e3d56..8b991b35f9 100644
--- a/cmd/pipecd/ops.go
+++ b/cmd/pipecd/ops.go
@@ -27,6 +27,7 @@ import (
 	"github.com/pipe-cd/pipe/pkg/admin"
 	"github.com/pipe-cd/pipe/pkg/app/ops/handler"
 	"github.com/pipe-cd/pipe/pkg/app/ops/insightcollector"
+	"github.com/pipe-cd/pipe/pkg/app/ops/orphancommandcleaner"
 	"github.com/pipe-cd/pipe/pkg/backoff"
 	"github.com/pipe-cd/pipe/pkg/cli"
 	"github.com/pipe-cd/pipe/pkg/datastore"
@@ -98,6 +99,12 @@ func (s *ops) run(ctx context.Context, t cli.Telemetry) error {
 		}
 	}()
 
+	// Starting orphan commands cleaner
+	cleaner := orphancommandcleaner.NewOrphanCommandCleaner(ds, t.Logger)
+	group.Go(func() error {
+		return cleaner.Run(ctx)
+	})
+
 	// Starting a cron job for insight collector.
 	if s.enableInsightCollector {
 		collector := insightcollector.NewInsightCollector(ds, fs, t.Logger)
diff --git a/pkg/app/ops/orphancommandcleaner/BUILD.bazel b/pkg/app/ops/orphancommandcleaner/BUILD.bazel
new file mode 100644
index 0000000000..8f2390615e
--- /dev/null
+++ b/pkg/app/ops/orphancommandcleaner/BUILD.bazel
@@ -0,0 +1,13 @@
+load("@io_bazel_rules_go//go:def.bzl", "go_library")
+
+go_library(
+    name = "go_default_library",
+    srcs = ["orphancommandcleaner.go"],
+    importpath = "github.com/pipe-cd/pipe/pkg/app/ops/orphancommandcleaner",
+    visibility = ["//visibility:public"],
+    deps = [
+        "//pkg/datastore:go_default_library",
+        "//pkg/model:go_default_library",
+        "@org_uber_go_zap//:go_default_library",
+    ],
+)
diff --git a/pkg/app/ops/orphancommandcleaner/orphancommandcleaner.go b/pkg/app/ops/orphancommandcleaner/orphancommandcleaner.go
new file mode 100644
index 0000000000..1afce08713
--- /dev/null
+++ b/pkg/app/ops/orphancommandcleaner/orphancommandcleaner.go
@@ -0,0 +1,79 @@
+package orphancommandcleaner
+
+import (
+	"context"
+	"time"
+
+	"go.uber.org/zap"
+
+	"github.com/pipe-cd/pipe/pkg/datastore"
+	"github.com/pipe-cd/pipe/pkg/model"
+)
+
+var (
+	commandTimeOut = 24 * time.Hour
+	interval       = 6 * time.Hour
+)
+
+type OrphanCommandCleaner struct {
+	commandstore datastore.CommandStore
+	logger       *zap.Logger
+}
+
+func NewOrphanCommandCleaner(
+	ds datastore.DataStore,
+	logger *zap.Logger,
+) *OrphanCommandCleaner {
+	return &OrphanCommandCleaner{
+		commandstore: datastore.NewCommandStore(ds),
+		logger:       logger.Named("orphan-command-cleaner"),
+	}
+}
+
+func (c *OrphanCommandCleaner) Run(ctx context.Context) error {
+	t := time.NewTicker(interval)
+	for {
+		select {
+		case <-ctx.Done():
+			return nil
+		case <-t.C:
+			start := time.Now()
+			if err := c.updateOrphanCommandsStatus(ctx); err == nil {
+				c.logger.Info("successfully update orphan commands status", zap.Duration("duration", time.Since(start)))
+			}
+		}
+	}
+}
+
+func (c *OrphanCommandCleaner) updateOrphanCommandsStatus(ctx context.Context) error {
+	timeout := time.Now().Add(-commandTimeOut).Unix()
+	opts := datastore.ListOptions{
+		Filters: []datastore.ListFilter{
+			{
+				Field:    "Status",
+				Operator: "==",
+				Value:    model.CommandStatus_COMMAND_NOT_HANDLED_YET,
+			},
+			{
+				Field:    "CreatedAt",
+				Operator: "<=",
+				Value:    timeout,
+			},
+		},
+	}
+	commands, err := c.commandstore.ListCommands(ctx, opts)
+	if err != nil {
+		return err
+	}
+
+	for _, command := range commands {
+		if err := c.commandstore.UpdateCommand(ctx, command.Id, func(cmd *model.Command) error {
+			cmd.Status = model.CommandStatus_COMMAND_TIMEOUT
+			return nil
+		}); err != nil {
+			c.logger.Error("failed to update orphan command", zap.Error(err), zap.String("id", command.Id), zap.String("type", command.Type.String()))
+		}
+	}
+
+	return nil
+}