The US not-for-profit news organisation clashed with the social media platform over its decision to describe the outlet as government-funded media.
NPR says it undermines its credibility, as US government funding accounts for less than 1 percent of its budget.
Twitter owner Elon Musk agreed to change the label on the BBC’s account.
The decision makes NPR the first major US news outlet to suspend its use of Twitter, despite the organisation having 8.8million followers on the platform.
The outlet encouraged people to instead subscribe to its newsletters and follow NPR on other social media platforms.
Mr Musk later reacted to the decision in a series of tweets criticising NPR and accusing the outlet of inconsistency in how it had previously described its funding model.
In one tweet on Wednesday night, Mr Musk tweeted a link to an NPR website in which it said that federal funding is important to public radio in the US.
It operates on a mixed-funding model that it says mostly includes corporate sponsorships, fees paid by NPR member organisations and donations.
Its decision to quit Twitter comes after the BBC disputed the same government-funded media label added to its @BBC account, which has now been removed. The BBC operates through a Royal Charter agreed with the UK government, which states the corporation must be independent.
Its public-service output is funded by UK households via a TV licence fee, as well as income from commercial operations.
