"You are actually a disgusting excuse for a president and we would love to have @BarackObama back", the message read.
It added, "We deleted the tweet, secured our account and are now investigating this".
The message was published on the company's corporate Twitter account at 6.16am EST on March 16 to its 151,000 followers and stayed online for around 20 minutes. After clinching the 1,237 delegates needed to win the Republican presidential nomination in May, Trump posted a photo of himself with McDonald's fries and an uneaten burger while riding on his airplane.
Even comedian Seth Meyers was seen to comment on the epic gaffe - referring to the company's mascot Ronald McDonald, he tweeted, "Clown on clown crime #McDonalds".
On Thursday morning, McDonald's tweeted negatively about Donald Trump - and lots of people are "lovin' it".
The Tweet was quickly deleted, but the screen shots remained. After an initial investigation, the social network said that an unidentified external source was behind the security breach.
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"I'll buy 100 McNuggets right now if you put the tweet back up", one person wrote on Twitter. The tweet comes from the company's corporate account; the brand account is @McDonalds.
That tweet included a new hashtag, #BoycottMcDonalds. An interesting fact is Trump has appeared in the television commercial for McDonald's alongside its character Grimace more than a decade ago. Others sad although they're not McDonalds fans, the tweet inspired them to stop in to the restaurant for the first time in years.
McDonald's CEO Steve Easterbrook has previously spoken favorably about Trump's presidency, specifically about his proposal to reduce business regulations. He has often tweeted pictures of him eating food from McDonald's and various other fast food chains.