The trailblazing Chan, nicknamed "Beef Ball" for her toughness, coached Eastern Sports Club to win Hong Kong's Premier League last April for the first time in 21 years and led them into this season's Asian Football Confederation (AFC) Champions League.
The 28-year-old announced her resignation Saturday after the final game of a disappointing season in which Eastern failed to add to their silverware and managed only one point in the Champions League group stages.
Eastern were outclassed in their continental campaign, scoring just one goal and conceding 24 in six group matches, including a 7-0 defeat at Chinese giants Guangzhou Evergrande.
An emotional Chan, who appeared close to tears, said Saturday she "must take responsibility" for failing to add any trophies this season and losing out in the title race to rivals Kitchee SC, according to the South China Morning Post newspaper.
Chan earned the AFC coach of the year award in her debut season in charge last year and a place in Guinness World Record as the first woman coach to win a men's championship in a top-flight football league.
She also made the BBC's prestigious list of the top 100 global women of 2016
Szeto Man-chun will replace Chan as head coach but she is expected to stay on with the club in a lesser coaching role.
Standout matches today