Cecotto began in kart racing before moving into open-wheel categories. He competed in the Formula BMW ADAC series in 2005 and then spent 2006 split between the German Formula Three Championship, where he took one victory, and the Formula Renault 2.0 Northern European Cup. In 2007, he entered the International Formula Master series and finished eighth overall with three podium finishes. Returning to the German F3 Championship in 2008, he placed third with two victories.
In 2009, Cecotto raced in the Formula Three Euroseries with HBR Motorsport before the team withdrew from races at Brands Hatch. He then signed with David Price Racing to compete in the GP2 Series alongside Michael Herck.
Cecotto's GP2 career stretched from 2009 through 2014 across multiple teams, producing mixed results before a standout 2012 campaign.
He joined Trident Racing for the 2009-10 GP2 Asia Series season but was replaced by Dani Clos after the opening round. He returned to Trident for the 2010 main series and scored his first championship points at Monaco before being replaced mid-season. The 2011 campaign, split between Super Nova Racing for the Asia series and Ocean Racing Technology for the main season alongside Kevin Mirocha and Brendon Hartley, yielded limited results with a fifteenth-place finish in the Asia series and twenty-fourth in the main series.
The 2012 season with Addax alongside Josef Kral was Cecotto's most competitive. After a difficult early part of the season, he surged at Monaco by taking his first GP2 pole position and winning the feature race. He followed this by winning the Hockenheim feature race after making a bold call to start on dry tyres on a damp but drying track. Despite seven retirements across the season, these two victories carried him to ninth in the championship — comfortably his best result in the series to that point.
In 2013, Cecotto's form dropped and he failed to reach the podium. He was again quick at Monaco, claiming pole for the feature race, but caused a multi-car collision at the first corner, ending his race and receiving a ban from the sprint race for causing the incident. He nonetheless had his most consistent points-scoring season with ten points finishes and 41 points in the championship.
Cecotto returned to Trident for 2014, his final full GP2 season. He scored two victories and three further podiums but faded in the latter stages, achieving a career-best fifth place in the final championship standings.
Cecotto was selected to participate in the young driver test at Yas Marina Circuit following the 2011 Abu Dhabi Grand Prix with Force India. In 2012 he again appeared in the young driver test, this time with Toro Rosso.
In 2016, Cecotto moved to the Formula V8 3.5 Series with RP Motorsport. He won his first race of the season at the Hungaroring but split from the team after the Spa round, leaving him without a seat for the remainder of the campaign.
Johnny Cecotto Jr.'s career carries added resonance given his father's status as a two-time motorcycle world champion and Formula 3 and touring car competitor. The Monaco victories in 2012 and a sustained presence across six GP2 seasons established him as a durable competitor in European junior categories, though his career never translated into a sustained higher formula opportunity. His 2014 fifth-place championship finish remains the high-water mark of his single-seater career.