GRU has two parallel runways. Runway 09R/27L is 3,000 metres (9,843 ft) long and 45 metres (148 ft) wide, while Runway 09L/27R is 3,700 metres (12,140 ft) long and 45 metres (148 ft) wide. The field elevation at the airport is 750 metres (2,459 ft) above mean sea level. There are high-speed exit taxiways on both runways that allow for traffic to depart the runway at higher speed to allow better efficiency for landing and takeoff traffic. Right now,there is an average of 650 takeoff and landing operations per day at the airport.

On 28 October 2015, the National Civil Aviation Agency of Brazil (Anac) authorized Airbus A380 operations at Guarulhos Airport, effective four days later. The authorization was granted after extensive works were conducted on the taxiways and special taxiing procedures were established.As of July 2016, there are still no regular A380 flights at São Paulo-Guarulhos, but on 14 November 2015 Emirates operated a one-time special flight with the "superjumbo" on its Dubai-São Paulo route to commemorate its eight years of operations in Brazil.