He had been in charge since 2013 and helped take the club to promotion to the National League South.
But form has been stop-start this season and after twice letting the lead slip at home to Hemel on Tuesday, they are now five games without a win.
The club sit 18th - just a point outside the relegation zone. The Bluebirds are without a game this weekend.
Chairman Neil Blackmore said: “In making this decision, I and my Board recognise and are extremely grateful for what Mark has achieved since his time as Manager at Chippenham Town FC and we wish him well for the future.
“We now need to move forward to appoint a new Manager as soon as possible.
“In the interim Head Coach, Gary Horgan, will take charge of the team.”
The club say they will provide further updates “as and when appropriate”.