Bill Maher has never married. Regarding marriage, Maher is quoted on his website as saying, "I'm the last of my guy friends to have never gotten married, and their wives—they don't want them playing with me. I'm like the escaped slave—I bring news of freedom."

In 2003, he began dating former Playboy Cyber Girl Coco Johnsen. In November 2004, at the end of their 17-month relationship, Johnsen sued Maher for US$9 million for "pain and suffering" for alleged "insulting, humiliating and degrading racial comments". Her suit stated that Maher promised to marry her and father her children, support her financially and buy a house in Beverly Hills. Johnsen's suit also alleged that she quit her job as a flight attendant and occasional model to be with him. Maher's lawyers in their response, filed on November 23, 2004, in Los Angeles Superior Court said Maher is a "confirmed bachelor, and a very public one at that" who "never promised to marry [Johnsen] or to have children with her". Maher's filing stated that, after the relationship had ended, Johnsen "launched a campaign to embarrass, humiliate, and extort ridiculous sums of money from Bill Maher". Johnsen had previously accused another former boyfriend of rape and kidnapping in 1997, and the charges were later dismissed for lack of evidence. The lawsuit was dismissed on May 2, 2005.

In 2005, Maher began dating Karrine Steffans, best-selling author and former hip hop model.

When commentators suggested there was a pattern to his dating because both his girlfriend and former girlfriend were black, Maher said, "People say I'm into black women. Robert De Niro is into black women. I'm just into women who are real, and they happen to be black." From 2009-11, Maher dated former adjunct professor, science educator, and current Skeptics' Guide to the Universe co-host Cara Santa Maria. In 2014, Maher was dating Ontario-born singer Anjulie Persaud.

In 2012, Maher purchased a minority ownership interest in the New York Mets.