Havenaar began his career with the Consadole Sapporo U-15 side, where his father played and later worked as goalkeeper coach.

[8] Havenaar made his first start for Vitesse on 4 February 2012 and provided an assist to Nicky Hofs first goal of the season, securing a 1–0 win NAC Breda.

[9] Havenaar scored his second goal for his new club in another losing effort, this time a 4–1 loss to title contenders FC Twente.

[10] Havenaar continued to impress for Vitesse, slotting the ball home after a cutting pass from Alexander Büttner to complete a 2–0 victory over De Graafschap on 4 March.

On 11 August 2015, Dutch Eredivisie side ADO Den Haag announced that they had signed Mike Havenaar as a striker.

[13] On 3 July 2017, ADO Den Haag officially announced that Havenaar would be leaving the club[14] to move back to Japan and join J1 league side Vissel Kobe.

[17] In 2007, Havenaar was picked to join the Japan U-20 squad to compete 2007 FIFA U-20 World Cup in Canada and played one match against Nigeria U-20.

[18] He made his debut for Japan on 2 September 2011 as a 70th-minute substitute against North Korea in a 2014 FIFA World Cup qualifier match,[19] striking the post.

He was brought up bilingual, speaking Japanese and his parents' native Dutch and learned fluent English at the Yokohama International School.