The airline said 200 of the 563 of the flights due to take off or land at 11 airports had been scrapped.
Unite, the union who called the strike, said the impact of the action was "severe", while BA said the fact that so many flights were still operating showed support for the strike was far from solid.
At Heathrow, 148 of 318 flights were cancelled.
Meanwhile at Gatwick four out of five flights were operating – some with makeshift crews.
A four-day second wave of strikes, over staffing and contract conditions, is due to begin is due to begin on Saturday.