Terri Hickey, a spokesperson for McDonald's, said: "Twitter notified us that our account was compromised".
Earlier this month, former presidential candidate Bernie Sanders savaged Trump with a single tweet and now the official McDonald's Twitter account has had a go.
His supporters are also boycotting Hawaii after a judge from the state temporarily halted Mr Trump's second travel ban. Now, the conservative Twittersphere is afire with #BoycottMcDonalds hashtags and Euro-Twitter is full of "I'd love to see Americans not eat McDonald's" jokes.
Has McDonald's taken one for the team and told Donald Trump what we've all wanted to say for SO LONG?
The tweet was deleted roughly 20 minutes after it was sent at 1.16pm GMT, but had already been screen-grabbed and widely shared across social media. The company focuses on promoting its food and business practices.
Trump's celebration dinner after winning the Republican nomination was a McDonald's burger, fries and a Diet Coke. The account only very rarely tweets anything but the most boring day-to-day updates related to the restaurant chain, and has never made a habit out of getting political in the past.
Trump, one of the more fast-food friendly presidents in recent history, tweeted pictures of himself eating fast food during the USA election campaign.
Hacking has been a persistent problem in recent years with the growing influence of Twitter and other social media sites.
He echoed those comments after Trump was elected, noting that uncertainty was likely to continue throughout Trump's transition.