After 51 games serving as the assistant, Yoshinaga was rewarded to lead Sagan Tosu U18 team the following season.
Yoshinaga was also the head coach of Yamanashi Gakuin Senior High School Soccer Club from 2010 to 2015.
On 14 April 2019, after first-team manager Koichiro Katafuchi resigns, Yoshinaga was appointed as his successor guiding them in the J2 League.
In his return in his first season, he steer the club to win the 2022 Singapore Premier League title.
After a string of disappointment results of five losing streaks, he left his post on 13 July 2024.