It comes only seven matches into the 2023/24 season with the club sitting 11th in the table on three points – their sole victory coming with a 3-2 triumph away to H&W Welders last month.
The 53-year-old took over at Dergview in May 2021 following a stint with Finn Harps U19s and guided them to a top-six finish during his first full season in charge.
Canning also won two consecutive North West Senior Cup crowns in 2021 and 2022 – the first tournament success in the club’s history – and they finished 10th last season.
His last game in charge would be Saturday’s 4-2 defeat away at Ards.
"Dergview Football Club have today accepted the resignation of 1st team manager Mr Tommy Canning,” the club posted on social media. “Tommy has worked tirelessly for the club delivering a top-six finish in his first season and two North West Senior cups.
"We would like to thank Tommy for his hard work and dedication during this time and wish him all the best for the future.
“We will now look to appoint a suitable replacement.”