After spending his early years karting in his native Germany, Theobald made his Formula Racing debut in the entry–level Formula König series in 2003, finishing the year in 12th position. The following season he scored nine podium places to be classified as runner–up behind Ronny Wechselberger, who won all 14 races in the championship.
In 2005, Theobald graduated to the German Formula Three Championship, racing in the same SMS Seyffarth Junior Team as his brother Julian. After failing to start either race at the fourth round at the Lausitzring, he switched from a Renault to a Mercedes–powered Dallara F304 for the remaining races. He scored three points to finish the season in 17th place. Theobald remained in the series for 2006, but due to budget constraints he competed in the secondary Trophy Class for older specification Dallara chassis. Despite again missing a round of the championship at the Lausitzring, he accumulated three class wins and a further eleven podium places to finish as runner–up behind Latvian Harald Schlegelmilch. In the overall standings, he finished tied on points with Natacha Gachnang and was classified in 14th place on countback. In 2007, Theobald originally started the season without a drive, but joined Christian Vietoris at Josef Kaufmann Racing for a one-off round at the Nürburgring, finishing the two races in 9th and 11th places respectively.
In October 2007, Theobald replaced Alessandro Ciompi at Eurointernational for the penultimate round of the Formula Renault 3.5 Series season in Estoril, lining up alongside his brother Julian in the team. He finished the two races in 25th and 19th places respectively.
In July2010, Theobald and his brother both took part in the FIA Formula Two Championship pre-event test at Brands Hatch. Whilst Julian took part in the Brands Hatch meeting, Johannes was unable to compete due to him undergoing his final university exams back in Germany. However, in September 2010, he did make his debut in the series, racing in the penultimate round of the season at Oschersleben. At the start of 2011, Theobald signed up with his brother to compete in a full season of the series.
