Ahmed joined the University of Dhaka as a lecturer on 28 March 1996 in the Department of Biochemistry and Microbiology.[8] He was promoted to assistant professor on 24 October 1997.[8] He was a postdoctoral fellow at the University of Pittsburgh from 1 December 1997 to 1999 and later worked as a research associate professor at the university.[8]
On 1 December 2004, Ahmed was promoted to associate professor.[8] In December 2007, he wore a black band as the acting general secretary of the Dhaka University Teachers Association protesting campus violence.[10]
Ahmed was promoted to full professor in December 2008.[8] He is a former general secretary of Dhaka University Teacher's Association.[7] He is an advisor to the Bangladesh Nationalist Party chairperson and former prime minister Khaleda Zia.[7] He served three terms in the senate of the University of Dhaka.[7] In May 2009, he was elected to the senate of the University of Dhaka as a candidate of the white panel, backed by the Bangladesh Nationalist Party.[11]
In 2017, Ahmed was appointed president of the Jatiyatabadi Samajik Sangskritik Sangstha following approval by Mirza Fakhrul Islam Alamgir, general secretary of the Bangladesh Nationalist Party.[12] In December 2022, he called for the release of Mirza Fakhrul Islam Alamgir from prison.[13]
Following the fall of the Sheikh Hasina led Awami League government, Ahmed was appointed pro-vice chancellor of the University of Dhaka in September 2024 replacing Professor Dr Sitesh Chandra Bachar.[14] In January 2025, students of seven colleges formerly affiliated with the University of Dhaka demanded his resignation and alleged Ahmed had misbehaved with them.[15][16] He later expressed regret for this.[17] He inaugurated the July Martyr Memorial Building, which is an extension of the Sheikh Mujibur Rahman Hall of the University of Dhaka.[18]