The prime minister granted permission on Sunday for the US to use British bases to target Iran's missile launchers and stores to help protect countries targeted by Tehran.
But the US president said he was "very disappointed" in Starmer for initially refusing to allow the use of the UK-US Diego Garcia base to target Iran.
Trump said it "took far too much time" for the prime minister to change his mind.
"President Trump has expressed his disagreement with our decision not to get involved in the initial strikes, but it is my duty to judge what is in Britain's national interest," Starmer told parliament on Monday.
The US had sought the use of the Diego Garcia base in the Indian Ocean and RAF Fairford in Gloucestershire for strikes against Iran.
The US president criticised the refusal to grant permission to use Diego Garcia for the initial wave of airstrikes against Iran's military and leadership.
"That's probably never happened between our countries before," he told The Telegraph.
"It sounds like he was worried about the legality."
Starmer said "that decision was deliberate" and "I stand by it".
"We all remember the mistakes of Iraq," he said.
"Any UK actions must always have a lawful basis and a viable thought-through plan."
In an apparent criticism of the US approach he said: "This government does not believe in regime change from the skies".
But Iran's retaliation to the US and Israeli attacks had threatened British people across the Middle East, prompting the decision to allow the bases to be used to hit Tehran's missile infrastructure.
"It is clear that Iran's outrageous response has become a threat to our people, our interests, and our allies and it cannot be ignored," he said.
Iran has hit targets across the Middle East, including in the United Arab Emirates, Qatar and Saudi Arabia, and there are fears Tehran has the ability to keep up its retaliatory actions for a week.
Around 300,000 Britons are believed to be in countries targeted by Iran, with 102,000 registering their presence with the Foreign Office as officials worked on contingency plans including a possible mass evacuation.
Starmer said the government was "looking at all options to support our people".
Hours after Starmer's announcement on Sunday about allowing the US use of bases, a drone hit RAF Akrotiri in Cyprus.
