The country music star's 'All My Rowdy Friends Are Back for Monday Night' is usually used as the introductory music on the football telecast.
While talking to Fox & Friends about the Republican Party candidates for the 2012 election, Williams Jr said that Speaker of the House of Representatives John Boehner playing golf with Obama was "like Hitler playing golf with [Israeli prime minister Benjamin] Netenyahu".
When challenged by the show's hosts who said they did not agree with the analogy, Williams Jr replied: "I'm glad you don't brother, 'cos a lot of people do."
Of the split in the country between the Republicans and Democrats, Williams Jr added: "We're more polarised than we've ever been. Guys, you know it. I'm not going to sugarcoat it."
When it was noted that he had used "the name of one of the most hated people in all of the world" to describe President Obama, he added: "That's true. That is true. But I'm telling it like it is. That just wasn't a good thing. It didn't fly."
A statement from ESPN read: "While Hank Williams, Jr is not an ESPN employee, we recognise that he is closely linked to our company through the open to Monday Night Football.
"We are extremely disappointed with his comments, and as a result we have decided to pull the open from tonight's telecast."
Watch Hank Williams Jr compare Barack Obama to Adolf Hitler on Fox & Friends below: