Baqai Medical University (Urdu: جامعہَ بقائی برائے علومِ طبابت) is a higher education institution located on M-9, Super Highway, Karachi, Pakistan.

The Baqais convinced the government that health delivery could be through a programme of community-oriented medical education.

In 1988, the first MBBS students were admitted, although it was not until 1990 that the Pakistan Medical and Dental Council formally permitted the college to start clinical teaching at Baqai Hospital, Nazimabad.

In establishing merit, entrance tests, interviews, extra curricular activities and school records are used.

Grants and scholarships are provided for faculty members to travel abroad to seminars and conferences and for higher education.