Checa began racing in the 125cc and 250cc classes for Honda in 1993. In 1995 he was called up as a replacement for Alberto Puig in the 500cc class after Puig broke both legs in a crash in France, and immediately demonstrated pace that impressed the paddock, nearly winning in Barcelona.
He continued in 500cc through 1998, the year of a near-fatal accident at Donington Park's Craner Curves. Initially thought to have suffered only minor injuries, Checa later lost his vision and required emergency surgery to remove his spleen, before making a remarkable recovery to miss just one race. He raced for Yamaha from 1999 onwards as Max Biaggi's teammate, developing a reputation for front-running speed undercut by a tendency to crash while leading — exemplified at Rio de Janeiro in 2002, where he fought from the back after stalling on the grid to reach the lead before crashing.
Checa raced with Yamaha factory machinery in 2003 and 2004, switched to Marlboro Ducati in 2005, and returned to the Tech 3 Yamaha satellite squad in 2006. His final MotoGP season came as the sole LCR Honda rider in 2007, at a time when Honda's 800cc machine was proving uncompetitive for non-factory riders. He made a brief return as replacement for Mika Kallio at the last two races of the 2010 MotoGP season.
Checa joined the Ten Kate Honda team in WorldSBK for 2008 as a replacement for departing champion James Toseland. He claimed his first two WorldSBK victories at Miller Motorsports Park in Salt Lake City on 1 June 2008, and also won the Suzuka 8 Hours with teammate Ryuichi Kiyonari. He finished fifth in the championship. His 2009 season with Ten Kate yielded four podiums and seventh place overall, and Ten Kate subsequently downsized and released him alongside Kiyonari.
Checa signed with the Althea Ducati team for 2010, scored the team's first-ever win at the season opener at Phillip Island, and finished third in that year's championship. The 2011 season was transformative: he dominated from the first round, winning both races at Phillip Island, and went on to claim fifteen victories across the year. He clinched the 2011 World Superbike Championship at the penultimate round at Magny-Cours in France, becoming the first Spanish champion and only the third European winner from outside the United Kingdom after Raymond Roche and Max Biaggi.
Checa's career is defined by resilience — surviving a potentially fatal accident in 1998, years of near-misses in the premier class, and a relatively late flourishing in WorldSBK that produced a title at 38 years old. His 2011 championship on the Ducati 1098R stands as one of the most complete season-long performances the series has seen, and his success confirmed the potential of privateer satellite teams to compete at the very highest level.