Pirro’s show Justice With Judge Jeanine did not air over the weekend, while the network’s schedule for next Saturday also omits the programme.
The president tweeted on Sunday about the host’s absence, saying she should be brought back.
“The Radical Left Democrats, working closely with their beloved partner, the Fake News Media, is using every trick in the book to SILENCE a majority of our Country,” Mr Trump wrote.
“Fox must stay strong and fight back with vigor. Stop working soooo hard on being politically correct, which will only bring you down, and continue to fight for our Country. The losers all want what you have, don't give it to them.”
Fox News has “strongly condemned” Pirro’s commentary on Ms Omar, a first-term Democratic representative from Minnesota.
She had questioned if the congresswoman’s decision to wear a hijab was “indicative of her adherence to Sharia law, which is in itself antithetical to the US Constitution”.
Fox said the comments did not reflect the network and it had addressed the issue with her, but did not specify what action had been taken.
Ms Omar, a practicing Muslim who was born in Somalia before moving to the US as a child, thanked Fox for its statement.
Writing on Twitter, she said no one’s commitment to the constitution should be questioned because of their faith or country of birth.
Pirro said her intention had been to start a debate, but that being Muslim did not mean someone did not support the Constitution. She has invited Ms Omar on her show.
Usually a frequent tweeter, the Fox News host has been absent from the social media site since her comments first aired.
Additional reporting by AP