Junshirō Kobayashi was initially a Nordic combined athlete. On December 14, 2007 he made his debut in Høydalsmo and finished 77th. On January 15, 2008 he won points in Iiyama in 18th place for the first time in the B-World Cup Nordic Combined. On January 10th, 2009 he made his World Cup debut in Val di Fiemme and finished in 52nd place. The next day he was 45. A little later Kobayashi started at the 2009 Junior World Championships in Štrbské Pleso and was 21st in the individual and eighth in the team. A year later he was again at the Junior World Championships , but here only in the individual, where he won the gold medal. The Junior World Championship was in Hinterzarten . After the 2009/10 season he ended his career as a Nordic combined athlete and switched to ski jumping.
For the first time he competed in the individual at the Junior World Championships 2011 in Otepää and finished in 18th place. At the end of the season Kobayashi started for the first time in the FIS Cup in Zaō and won both competitions. As a combined competitor, he had participated in several FIS races in Japan since 2008 . On July 2nd, 2011 Kobayashi jumped in the Continental Cup for the first time in Kranj and was able to collect his first points with 14th place. After he was able to achieve two excellent placings a week later on the Brunnentalschanze in Stams with third and fourth place, he switched to the higher-class Summer Grand Prix . In his second competition on July 20, 2011 in Szczyrk , Poland , he took tenth place. After further top ten placements, he reached 23rd place in the overall ranking of the Grand Prix. Kobayashi made his World Cup debut on November 27, 2011 in the team competition on the Rukatunturi hill in Kuusamo , Finland , when he finished second with the Japanese team. On the same day he also made his debut in the individual competition, in which he was able to achieve his first World Cup points straight away as 24th. His best individual placement in the World Cup this season was 16th in Bischofshofen . He finished his first World Cup season as 52nd overall with 40 points. After he was able to get 17 World Cup points again in the 2012/13 season , he only started as part of the national group in Sapporo in the World Cup in the 2013/14 season , where he missed the points twice. At the 2013 Winter Universiade in Predazzo , Italy , he took fourth place on the normal hill. In the mixed team competition he was fifth and fourth in the team competition. In the individual competition on the large hill, he won the bronze medal behind Krzysztof Biegun and Sami Niemi .
In the summer of 2014, Kobayashi achieved several top ten placements in the Grand Prix and thus finished sixth in the overall standings. From the 2014/15 season he jumped regularly in the World Cup again. On March 12, 2015, he achieved his best result in the World Cup to date as 13th in Trondheim, Norway . In the overall World Cup he also achieved his best career result to date with 44th place. At the Winter Universiade 2015 in Štrbské Pleso , Slovakia , he finished fifth in the individual competition on the normal hill. With his sister Yuka Kobayashi he won the mixed team competition and with his compatriots Kanta Takanashi and Minato Mabuchi he won the silver medal behind Russia in the men's team competition on the normal hill. At the Nordic World Ski Championships in Falun in 2015 , he took 25th place on the normal hill and 13th place on the large hill in the two individual competitions. With the Japanese team he was fourth.
On September 13, 2015, he won his first Summer Grand Prix competition on the Gorney Gigant in Almaty, Kazakhstan . In the 2015/16 and 2016/17 seasons he only reached the points in the World Cup a few times and did not get beyond 17th place in Sapporo in these two years.
On August 26 and 27, 2017, he won both Grand Prix competitions in Hakuba . He won the second competition before his brother Ryoyu . He finished third in the 2017 Summer Grand Prix and thus with the best result of his career to date. On November 19, 2017, Kobayashi surprisingly won his first World Cup victory at the opening competition of the 2017/18 season in Wisła , after only 13th place was his best World Cup result. He finished the Four Hills Tournament in 2017/18 in fourth place in the overall standings after jumping among the top ten in all four competitions (places 6, 4, 6 and 7). In January 2018, he took part in the ski flying world championship in Oberstdorf for the first time , placing 29th in the individual competition. At the 2018 Winter Olympics in Pyeongchang , he took part in two of three competitions. In the individual competition on the normal hill , he finished 31st and in the individual competition on the large hill , he was 24th . He was not used in team jumping on the large hill . In addition to his victory at the start, he achieved a few more top ten placements in the World Cup and completed by far his best World Cup season. He finished eleventh in the overall World Cup with 568 points. At the 2019 World Championships in Seefeld in Tyrol , he won the bronze medal in team jumping with his teammates Daiki Itō , Yukiya Satō and Ryōyū Kobayashi . In the individual competitions he took 17th place on both the large and normal hill.