Sharbat Gula could now face a fine and up to 14 years in jail.
Officials say she was arrested by Pakistan's Federal Investigation Agency (FIA) after a two-year probe in Peshawar, near the Afghan border.
Pakistan recently launched a crackdown against fake IDs.
Mrs Gula applied for an identity card in April 2014, using the name Sharbat Bibi. If the fraud allegations are true, she is one of thousands of Afghan refugees living in Pakistan who have tried to dodge its computerised system.