More than 6.8 million people are known to have been infected in the US, more than in any other country.
The milestone comes amid an increase in cases in a number of states, including North Dakota and Utah.
In March, President Donald Trump said if deaths were between 100,000 and 200,000, the country would have done a "very good job".
The previous month, when 15 cases had been reported in the country, he predicted that the number was going to be "close to zero" within a couple of days.
JHU reported the new death toll of 200,005 on Tuesday. The university has been collecting US and global coronavirus data since the outbreak began late last year in China. The first case in the US was confirmed in January.
President Trump's administration has been repeatedly criticised over its handling of the outbreak.
"Due to Donald Trump's lies and incompetence in the past six months, [we] have seen one of the greatest losses of American life in history," Democratic presidential candidate Joe Biden said on Monday.
"With this crisis, a real crisis, a crisis that required serious presidential leadership, he just wasn't up to it. He froze. He failed to act. He panicked. And America has paid the worst price of any nation in the world."
But on the same day, Mr Trump said he and his administration had done "a phenomenal job" and gave himself an "A+" for his handling of the pandemic.
He said the US was "rounding the corner on the pandemic, with or without a vaccine".