Bilal Aybakan graduated from Marmara University's Faculty of Theology in 1985. In 1990, he completed his MA thesis, titled "The Contract of Mandate in Islamic Law," followed by the conclusion of his PhD thesis, "The Fulfillment of Obligations in Islamic Law," in 1997. Progressing in the field of Islamic law, he attained the rank of associate professor in 2002 and became a full professor in 2007. Over 25 years, he taught various courses on diverse aspects of Islamic law in both undergraduate and graduate programs. Aybakan authored numerous scholarly publications in both Turkish and English, covering various dimensions of Islamic Jurisprudence.

His tenure at Marmara University concluded on March 27, 2017, where he served as the head of the Department of Islamic Law. Immediately afterward, on the same day, he joined Ibn Haldun University's academic staff. Assuming the role of founding dean of the Faculty of Islamic Sciences, he maintained this position until December 20, 2023. Currently, Bilal Aybakan holds a full-time position at the same faculty as a professor specializing in Islamic jurisprudence.