The sixth season of the American comedy television series Scrubs premiered on NBC on November 30, 2006 and concluded on May 17, 2007 and consists of 22 episodes.

Guest stars in the sixth season included Keri Russell and Michael Weston.

J.D., for instance, is cast in the role of expecting father since his girlfriend, Dr. Kim Briggs (Elizabeth Banks), is pregnant with his child.

Dr. Cox, as father of two children with Jordan, struggles to prevent his foul disposition from affecting his parenting.

Even though Eric Weinberg and Sean Russell each wrote an episode this season, they were not part of the writing staff.