Yes, you can. But, only order with card payment methods can be refunded directly. Steps to refund order as follows:

1.  Dashboard Xendit > Accept Payments > Credit/Debit Cards > Charges > click on the particular transaction
2.  You can refund the payment by clicking Refund on the order details.
3.  You can specify how much you want to refund on the refund window.
4.  You will see that the refunded amount is deducted from the payment total.
5.  Upon full or partial refunds, the payment status will change to “Refunded”  at Xendit dashboard > Accept Payment > Credit / Debit Cards

For more info, you can refer to the documentation here