Walsh had started working in Pakistan in 2004 for the UK's The Guardian, and switched to the NY Times last year.
“Here I go. Hard to believe this is happening,” the 39-year-old tweeted early Sunday after filing his last report on the country's landmark general elections.
He was dropped at the airport by Pakistani columnist Cyril Almeida and escorted by a convoy of security officials' vehicles. He later tweeted messages of thanks to friends and well-wishers.
The expulsion order stated: “It is informed that your visa is hereby cancelled in view of your undesirable activities,” according to the Times.
Walsh has written about the country's political strife, its insurgency and its sometimes tense relations with the United States.
“72 hours, wheels up,” he tweeted. “To all friends, especially in Pakistan, who offered overwhelming support in recent days, thank you so much.”
Jill Abramson, the newspaper's executive editor, sent a letter to Pakistani authorities describing Walsh as a “reporter of integrity who has at all times offered balanced, nuanced and factual reporting on Pakistan”.
She called the accusation of undesirable activities “vague and unsupported.”
Undesirable activities could be pretty much anything in a Muslim land.