The team is coming off a 79-59 loss to McNeese State, marking their third straight and fourth of the last five games. Stephen F. Austin is currently 1-7 in conference play, ranking second-to-last in the Southland Conference.
Associate head coach Tony Jasick will serve as the interim head coach for the rest of the season.
"We want to thank Kyle for his positive contributions and leadership over the past nine seasons, including memorable and iconic wins at some of the most hallowed sites in college basketball that will forever be etched in SFA history," said Athletic Director Michael McBroom said in a news release. "We wish him well in his future opportunities."
Keller had a 171-95 overall record as the Lumberjacks' head coach. He led the school to an NCAA Tournament birth during the 2017-2018 and was Southland Conference Coach of the Year for the 2019-2020 season, one in which the team went 28-3.
The team has only had two losing seasons under Keller as head coach, 2018-2019 season and this year.