The vote had been seen as a key test of how well the new president will be able to push through other planned reforms.
Promises of tax cuts and higher infrastructure spending have lifted stocks in the US since the election.
However, the proposals to replace Obamacare failed to gain enough support to pass in Congress.
The Dow Jones fell 59.86 points to 20,596.72, while the wider S&P 500 index dropped 1.98 points to 2,343.98.
The tech-heavy Nasdaq index was 11.04 points higher at 5,828.74.
Financial markets seem to have taken the view that the pulling the healthcare bill does not mean the end of President Trump's entire reform agenda.
Investors are hoping he will now press ahead with his economic agenda, including tax reform.
"Now that they've taken the healthcare issue off the table, I think the market is more optimistic that they can do other things that are more doable that are not so complicated, such as regulatory reform and lowering taxes," said Margaret Patel, senior portfolio manager at Wells Fargo Asset Management in Boston.
And after the vote was dropped the Speaker of the United States House of Representatives, Paul Ryan said: "This does make tax reform more difficult but it does not make it impossible."
On the Nasdaq, shares in Micron Technology ended the day 7.4% higher at $28.43 after the chipmaker reported better-than-expected results on Thursday.
The company said it had benefited from rising prices for memory chips, and it reported profits of $894m for the three months to 2 March.
(Close): It was a mixed picture at the close on Wall Street after a vote on President Donald Trump's healthcare reform bill was withdrawn.