The 39-year-old's highly-successful two-year spell at St Jakob's Park will come to an end after Sunday's home game with Lausanne
The 39-year-old took over the reins at the club in October 2012 and has led the team to a period of success, including runs to the Europa League semi-finals last term and quarter-finals this campaign.
However, he has elected to move on this summer, a club statement has confirmed.
"Coach Murat Yakin and the club's manangement have decided together that they will not continue their successful cooperation in the 2014-15 season," it read.
Under Yakin's tutelage, Basel won the Swiss Super League in 2012-13 and 2013-14, as well as the national cup last term.
During this season's Champions League group stage, Basel beat Chelsea both home and away.
Yakin's final game this season is against Lausanne at home on Sunday.