Chapdelaine's offence struggled for long stretches during the second half of the 2013 season after starting quarterback Travis Lulay went down with a shoulder injury.
The Lions, who lost in the CFL West Division final to the Saskatchewan Roughriders, were criticized for a lack of imagination under Chapdelaine's leadership, with the running game practically non-existent for long stretches.
"Jacques has been a big part of our past success," B.C. head coach Mike Benevides said in a statement. "He presided over two championship offences and two most outstanding players during his time with the club and I am grateful for his hard work and dedication during our time together.
"At this time however, we agree that it is in the best interest of both parties to proceed in a new direction."
The 52-year-old started his career with the Lions in 2003 as the team's receivers coach and was promoted to offensive co-ordinator in 2005 under former head coach Wally Buono.
After B.C. won the Grey Cup in 2006, Chapdelaine became the offensive co-ordinator of the Edmonton Eskimos. He returned to the Lions the following year as receivers coach and got his old job back as offensive co-ordinator in 2010, helping the team win another Grey Cup in 2011.
"After taking some time to reflect on this past season, I've concluded that both I and the B.C. Lions need a change moving forward," said Chapdelaine, who has been linked to the head coaching job with the expansion Ottawa Redblacks. "It has been a great privilege to work with Lions players, coaches and many other members of this outstanding organization."