Gemperline joined the chemistry faculty at East Carolina University (ECU) as an assistant professor in 1982. He was promoted to full professor in 1993. According to The Daily Reflector he had a long and distinguished teaching and research career at ECU with "more than 30 years of research experience in chemometrics involving 38 undergraduate students, 20 master’s students, nine visiting doctoral students and six post-doctoral research assistants" and  "more than 60 publications in the field and more than $1.8 million in external grant funds." He also is one of three inventors listed on a licensed patent for designing optical filters for chemical calibration. He received the Helms Award for Outstanding Research from the East Carolina University Chapter of Sigma Xi in 1987, the East Carolina University Distinguished Research Professor of Chemistry (award for 5-year achievement and permanent title) in 1999, and in 2001 was made an East Carolina University College of Arts and Sciences Distinguished Professor of Chemistry, an award for lifetime achievement and permanent title, given in recognition of "outstanding teaching and advising, research and creative productivity, and professional service."
In 2003 Gemperline joined the university administration as associate vice chancellor of research and graduate studies. He became dean of the Graduate School in 2008 and remained in that position until his retirement in 2022. Gemperline served in the positions of president-elect (2009-2010), president (2010-2011), and immediate past president (2011-2012) of the North Carolina Council of Graduate Schools.