The airline did not operate 331 flights after cancelling 248 on Wednesday.
Some passengers have been stranded in European cities after Easter breaks, prompting Easyjet to operate five "rescue" flights on Friday.
The flights will bring three parties of schoolchildren back to the UK.
The additional flights will run from Luton to Paris, Paris to Barcelona, Barcelona to Luton, Gatwick to Madrid, and Marrakech to Gatwick.
Easyjet says it will put larger aircraft on routes that have been most affected to allow more passengers to get home.
A spokesman said the "unnecessary" strike had caused "considerable and disproportionate disruption for passengers and airlines across Europe".
Rival low-cost airline Ryanair said it had been forced to cancel more than 500 flights over the last two days.
"We again call on the EU [European Union] and French authorities to act now and prevent  thousands of travellers being held to ransom by these French [air traffic control] workers," the Irish airline said.
Johanna Booth, from Liverpool, has been stuck in Barcelona after two Ryanair flights were cancelled due to the industrial action.
"We have a four-month-old baby and his formula milk has ran out and he is not drinking much of the other variety, so I am concerned," she told the BBC.
"The support we have received from Ryanair has been minimal."
Air France said it was operating one-in-four flights to and from Orly airport in Paris, about 40% to and from cities in the rest of France, and 50% of medium-haul flights to and from Paris-Charles de Gaulle airport.
No long-haul Air France flights were affected on Thursday.
Air traffic controllers are planning further industrial action from 16 to 18 April and from 29 April to 2 May 2 - both key holiday periods.
Roger Rousseau, head of the SNCTA union that represents French air traffic controllers, said: "We can assure our passengers that we are doing everything possible to limit the inconvenience of this strike on them."
Among the issues upsetting members is that the retirement age will be raised from 57 to 59.
Easyjet has cancelled hundreds of flights as the second day of strike action by French air traffic controllers took its toll.