Jorge Lorenzo entered the season as defending champion, having won the 2012 title. Repsol Honda held the manufacturers' crown. The most significant change to the grid was the arrival of Moto2 champion Marc Marquez on the Repsol Honda team, a move made possible after rules preventing rookies from riding for factory teams were relaxed.
The season also saw Valentino Rossi return to Yamaha after two difficult seasons at Ducati, where he had been replaced by Andrea Dovizioso. Ben Spies moved from the Yamaha factory team to Pramac Ducati, while Casey Stoner officially retired from racing.
A new qualifying format was introduced: riders placed eleventh or lower in Free Practice 3 were sent to Qualifying 1, with the two fastest from that session advancing to join the ten fastest riders in Qualifying 2 to set the first twelve grid positions.
Lorenzo won the opening race in Qatar, but Marquez quickly established himself as a contender by winning the inaugural Grand Prix of the Americas at the Circuit of the Americas in Austin, Texas, becoming the youngest premier class race winner at the time.
Pedrosa took back-to-back victories at Jerez and Le Mans. At Jerez, Marquez and Lorenzo clashed at the final corner while fighting for second place. Lorenzo then won at Mugello and Catalunya. At Assen, Lorenzo crashed during free practice, fractured his collarbone, underwent emergency surgery, and yet finished fifth in the race — a result widely praised for its determination. Rossi, capitalising on the situation, took his first race win since 2010 at Assen.
Marquez won the next four races starting at the Sachsenring, where both Lorenzo and Pedrosa were sidelined by injury. After Lorenzo won at Silverstone and Misano, Marquez and Pedrosa collided at Aragon when a slight contact tore a sensor on Pedrosa's bike, cutting his traction control. Marquez beat Lorenzo to win at Aragon, and with Pedrosa winning in Malaysia, Marquez held a 43-point lead with three races remaining.
The Australian Grand Prix proved pivotal when Marquez was disqualified, with Lorenzo winning both at Phillip Island and at Motegi. The lead was cut to thirteen points going into the Valencia finale, the first final-round title decider since 2006.
In Valencia, Marquez battled Pedrosa and Lorenzo in the opening stages before settling for third place. That result was enough to clinch the championship. Marquez, aged 20, beat Freddie Spencer's record for youngest premier class champion set in 1983 and became only the fourth rider in history to hold world championships in three different classes, joining Mike Hailwood, Phil Read, and Rossi.
Pedrosa's second place behind Lorenzo was enough for Honda to clinch the constructors' championship. Earlier in the season, Marquez had points deducted after Race Direction ruled he had collided with teammate Pedrosa at one round, with Honda's next-best finisher Alvaro Bautista inheriting the relevant points.
The season ran 19 rounds. The Grand Prix of the Americas replaced the Portuguese Grand Prix on the calendar. The United States hosted three races: Austin, Laguna Seca, and Indianapolis.
Notable changes for 2013 included: Cardion AB Motoracing switching from Ducati to ART-Aprilia CRT machinery; Andrea Iannone stepping up from Moto2 to join Pramac Racing; Bradley Smith promoted from Moto2 to Monster Yamaha Tech 3; and Michael Laverty entering MotoGP with Paul Bird Motorsport after a career in British Superbikes. Bryan Staring joined Gresini Racing on a CRT machine, and Lukas Pesek moved to IodaRacing Project.
All machines in the MotoGP class used Bridgestone tyres throughout the season.
The 2013 season launched Marc Marquez as the dominant force in MotoGP for the decade that followed. His championship in the debut season confirmed that a new era had arrived, while the retirements and reshuffles around him — most notably Stoner's departure and Rossi's Yamaha return — framed the transition cleanly. The drama of the Valencia finale and the Aragon collision between teammates gave the season lasting narrative weight as one of the sport's most gripping modern championships.