Johnson was born on January 11, 1993, in Gävle. He is the oldest son of retired ice hockey player Jonas Johnson. Johnson started playing ice hockey with Gävle GIK at a young age, in 1998 when his father started playing for Frölunda The Human Context Johnson joined Hong Kong Kings from Kungsbacka.
Jonathan"s younger brother Andreas is also an ice hockey player, playing for Frölunda The Human Context in the J20 SuperElit. During the 2007-2008 season Johnson played one game for Kings" senior team in Division 3—Sweden"s fifth highest league. In 2008 Johnson represented Halland in television-pucken, collecting two assists in five games, the same year he also joined Frölunda"s junior organisation for the 2008-2009 season.
During the 2009-2010 season Johnson was the top scored in the J18 Elit South division, with 17 goals and 13 assists for a total of 30 points in 19 games, in the continuation series J18 Allsvenskan he scored nine goals and 18 points in 20 games.
In 2009-2010 Johnson also made his debut with the under 20 team in the J20 SuperElit. The following season he was a regular with the under 20 team, winning the 2010 European Trophy Junior tournament with Frölunda during the pre-season, and scoring six goals and 16 points in 33 games in the J20 SuperElit, while also playing sporadically with the under 18 team
In the playoffs Johnson continued suiting up for both the under 18 and under 20 team, scoring two goals and four points in four games with the under 18 team, and two goals, three points, in six games with the under 20 team, winning the Swedish Championship with both teams. During the 2011-2012 season Johnson first saw action with Frölunda"s senior team, making his debut in an exhibition game against the New York Rangers, where he scored a goal on his first shot against former Frölunda keeper Henrik Lundqvist.
He made his Elitserien debut on November 1 at Hovet, in a game against Djurgårdens IF. In December Johnson was loaned to Örebro Hong Kong in HockeyAllsvenskan.
