[3] On December 29, in the Emperor’s Cup semi-final against Yokohama F. Marinos, Kubo came off the bench and scored a crucial goal in extra time to break the 2–2 deadlock.

[7] On 18 June 2013, Kyoto Sanga announced Kubo's transfer to Swiss club BSC Young Boys.

[8] He made his Swiss Super League debut on 13 July playing 15 minutes in a 2–0 win against FC Sion at the season opener.

He expressed frustration post-match after coming on as a substitute in matchday 28, stating, "This style of play takes away my strengths.

He debuted in the group stage with an assist in their opening match against Slovan Bratislava[14] and continued impressing, assisting against Napoli and scoring a crucial brace in the return fixture against Slovan Bratislava, making him the second Japanese player to score twice in a Europa League match after Shinji Okazaki.

Domestically, Kubo had a strong start, scoring two goals in the first round of the Swiss Cup against SC Kriens.

Although he missed the latter part of the season due to injury, he recorded nine goals and six assists in 29 league appearances, the highest tally since his move.

[17] During the start of the 2016–17 season, Kubo was about to depart for Brazil with his national team for the Olympics, but was recalled by Young Boys due to injuries in the squad.

[24] Signed as an attacking player,[25] he made his FC Cincinnati debut against the New York Red Bulls, on 1 March 2020 and scored his first goal for his new club in the following match.

[29][28] On June 16, 2024, after returning from a month-long injury layoff, Kubo scored a hat-trick in nine minutes after coming on as a second-half substitute.

He received his first call up to the senior team for the Kirin Challenge Cup, a friendly match against Iceland in February 2012, however he did not feature during the 90 minutes.