He married Yasmeen Haque in 1978. She is currently the Dean of the Life Science Department and Head of the department of Physics at Shahjalal University of Science and Technology (SUST). They have a son, Nabil, and a daughter, Yeshim. Iqbal's elder brother, Humayun Ahmed, was a writer and filmmaker. His younger brother, Ahsan Habib, is the editor of the satirical magazine, "Unmad" ("Mad") and a cartoonist.