The Okhla legislator, who was also a member of the State Haj Committee, sent his resignation letter to Chief Minister Arvind Kejriwal.
His resignation came two days after the Anti-Corruption Branch of the Delhi government raided the Delhi Waqf Board office here in connection with an alleged recruitment scam involving Khan.
In his letter, Khan stated that he has "run out of patience" of issuing clarifications to the public pleading innocence over a number of allegations levelled against him and his family members.
Speaking in the Delhi Assembly yesterday, Khan defended himself saying he had made the "contractual" recruitments following due procedures. Waqf Board was reeling under shortage of staff which necessitated the appointments, he said.