Direct action group Plane Stupid said 13 demonstrators opposed to the airport's expansion plans with a third runway got on to the northern runway.
Six protesters have been arrested on suspicion of Aviation Act offences, Scotland Yard said.
The runway was closed for nearly three hours and 13 flights were cancelled.
The airport apologised for the disruption caused and advised passengers to check with their airlines before they travel.
The airport's southern runway remained open throughout the protest.
A Heathrow airport statement said: "We are working closely with the police who are dealing with the incident. Both runways are open although there will still be delays - we are sorry for the disruption to passengers.
"Our priority remains to ensure the safe running of the airport."
On July 1, a report recommended a new runway should be built at Heathrow rather than Gatwick.
The idea of expanding Heathrow has always been surrounded by controversy because of its location in a heavily built-up area. Nearly 800 homes would have to be demolished to build the new runway.
Heathrow, which serves 185 destinations in 84 countries, handled 73.4 million passengers in 2014.
