In a statement on their website the 2015-16 champions confirmed that Chan, also known as “Beefball”, had left with immediate effect and would be replaced by Wong Chun-yu.
The statement confirmed that Chan had resigned from her post on the back of a run that saw the team win only one of their past 10 matches.
Before returning this season Chan managed the side from December 2015 to May 2017, including winning the HKPL title and taking the club to their first ever continental campaign in the AFC Champions League.
Chan was awarded with the AFC Women’s Coach of the Year honour in December 2016.
She took over Eastern in 2015 and in 2016 she became the first woman to coach a men’s team to a title in a top-flight continental competition.
Chan had earlier resigned in 2017 as she looked to get her coaching badges but returned to the role 14 months later last July.
Eastern sit second in the table, a point behind leaders Hong Kong R&F. Their next game is against Southern on February 17.