The season tactician took the decision two days after the Akure Gunners failed to grab a Caf Confederation Cup ticket after their 0-0 draw against champions Enyimba at the Teslim Balogun Stadium, Lagos.
Sunshine Stars finished in sixth place despite making a blistering start in the just concluded Nigeria topflight.
“I will like to inform you that I have stepped down as coach of Sunshine Stars,” Boboye told Goal.
“No regrets for the decision having helped the team finish well in the just concluded season. This has nothing to do with our inability to qualify for the Confederation Cup.
“For me, a new start seems to be the best solution for all parties and I believe the next manager will benefit from the structure I left behind.
“I will like to thank the Ondo State Football Agency for giving me the privilege to manage the team after my heart. Appreciations also to my technical crew, players and teeming fans of Sunshine Stars for standing by me throughout my stay.
“Wishing the team all the best in the Nigeria Premier League next season and I believe they have all it takes to win the league next season,” he concluded.
Coach Boboye who refused to disclose his next move is currently in Abuja for his Caf coaching B licence. In charge of the Akure based outfit, he recorded over 30 wins, six draws and just 14 defeats.
While with the team, the likes of Ikechukwu Ezenwa, Paul Onobi, Seun Olunlayo, Eze Stephen, Prince Aggreh, Tunde Adeniji and Dayo Ojo were invited to the Super Eagles – the highest number to be invited to the senior national team in the history of Sunshine Stars.