Speaking at a White House press briefing on Monday evening, the president also got the year the pandemic started wrong.
“The closest thing is in 1917, they say, the great pandemic,” Mr Trump told reporters.
“It certainly was a terrible thing where they lost anywhere from 50 to 100 million people, probably ended the Second World War,” he added.
The Spanish Flu began in 1918, with the first infections recorded around March that year.
The pandemic lasted until 1920 and did, as Mr Trump alluded to, kill millions of people.
But WWII did not break out until 1939 when Hitler invaded Poland. Britain and France declared war two days later, sparking a conflict that would last six years.
The war ended in 1945 when the Axis powers surrendered.
Japan surrendered unconditionally in August 1945 after the US had dropped an atomic bomb on Hiroshima.
White House officials said that the president misspoke and had, in fact, been referring to WWI which began in 1914 and ended in 1918.
According to Peter C Wever and Leo van Bergen, the Spanish Flu greatly affected all sides during WWI, claiming thousands of lives.
“The disease had a profound impact, both for the military apparatus and for the individual soldier,” the pair wrote in a paper published in the Influenza and Other Respiratory Viruses journal.
However, Wever and van Bergen were reluctant to conclude that the pandemic brought an end to or changed the course of the war.
“It struck all the armies and might have claimed toward 100,000 fatalities among soldiers overall during the conflict while rendering millions ineffective,” they added.
“Yet, it remains unclear whether 1918 pandemic influenza had an impact on the course of the First World War.”
Monday’s error was the second verbal blunder the president has had in a matter of days.
Last week, Mr Trump pronounced Thailand and “Thighland” when delivering a speech at Whirlpool factory in Ohio.
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