Maloney left Easter Road following Saturday’s 2-1 defeat against Edinburgh rivals Hearts in the Scottish Cup semi-final.
“Our hope in appointing Shaun Maloney as a young, highly regarded coach was that he would help us take the club forward, but ultimately it didn’t work out,” Hibernian chairman Ron Gordon said.
“We thank Shaun and his coaching staff for all their hard work and efforts and wish them all the best for the future.”
Former Celtic and Scotland midfielder Maloney quit his role as Belgium assistant manager to succeed Jack Ross at Hibernian in December.
The 39-year-old won his first two matches against Aberdeen and Dundee United.
But Hibernian had managed just one league victory since then, and a 3-1 defeat against Hearts the week before the semi-final loss consigned them to a bottom-six finish.
Maloney has been without key players at times through illness, injury and suspension, while the club sold Australia winger Martin Boyle to Saudi Arabian side Al-Faisaly late in the transfer window.
Former Hibernian skipper David Gray will take caretaker charge for the remainder of the season, with support from Eddie May and Jon Busch.