Yes, a CIS tax refund is processed as part of your Self Assessment tax return. When you complete your tax return, you must include all your income and allowable expenses, as well as the CIS deductions that have been made by contractors throughout the year. The tax you’ve already paid through CIS deductions will be credited against your overall tax liability for the year. If your CIS deductions exceed your tax due, HMRC will issue you a refund for the difference.