In an appearance on "Fox & Friends" that aired on Friday, Trump said he would like Pelosi to stay right where she is because she has an "extraordinary record against her."
"It would be a very, very sad day for Republicans if she steps down. I would be very disappointed if she did," Trump said.
The comment came after some Democrats on Thursday called for Pelosi to step down in the wake of special election losses this year, including a high-profile race in Georgia on Tuesday.
Republican Karen Handel beat Democrat Jon Ossoff in the race for the Georgia seat vacated by Health and Human Services Secretary Tom Price, dashing Democratic hopes to pull off an upset in the runup to the 2018 midterm elections.
The two campaigns and outside groups supporting and opposing the candidates shelled out at least $36 million, including more than $22 million from Ossoff's campaign.
Pelosi, speaking to reporters on Thursday, said she's confident she has the support in her caucus.
—The Associated Press and CNBC's Jacob Pramuk contributed to this report.