At least three Republicans - John McCain, Susan Collins and Lisa Murkowski - voted against the bill, which needed a simple majority to pass.
President Donald Trump said the three had "let the American people down".
The so-called "skinny" repeal, which would have scaled back some of the more controversial provisions, is the third failed attempt to repeal Obamacare.
It would have resulted in 16 million people losing their health insurance by 2026, with insurance premiums increasing by 20%, according to the Congressional Budget Office (CBO).