Syed Khwaja Khairuddin (Urdu: سيد خواجہ خير الدين, Bengali: সৈয়দ খাজা খায়েরউদ্দিন) was a Pakistani politician.

[5] He was a polling agent of Fatima Jinnah in Dhaka for the 1965 Pakistani presidential election which she contested for against President Ayub Khan.

He was accused in the National Assembly of Pakistan for political bias in appointing personnel during his tenure as mayor.

[11] After migrating to Pakistan, he served as Secretary General of the Movement for the Restoration of Democracy (MRD) which was an alliance of eight parties against President Muhammad Zia-ul-Haq.

[2] Dr. Syed Khawaja Alqama, Khairuddin's son and the former vice chancellor of Bahauddin Zakariya University, was nominated to be Pakistan's High Commissioner to Bangladesh.