On April 16, 2009, Bill Lawrence wrote on the abc.com message boards that a season 9 of Scrubs was still "50/50."[57] On April 28, 2009, it was announced that ABC was in talks to renew Scrubs for another year,[58] however, if this were to happen, some of the cast may or may not be back [due to other commitments], or only back part time.

Bill Lawrence also stated that Scrubs as we know it is over, although there are possibilities for the show to move forward with a new cast in an ER type role on ABC, or take a new title completely. To any who disagreed with it, saying it would tarnish Scrubs' legacy, Lawrence was quoted saying "'Legacy shmegacy.' I'm really proud of the show, I'll continue to be proud of the show, but I love all of those people..."[59]

On May 14, 2009, it was announced that Zach Braff has signed to be on Scrubs for six episodes to transition the show to its new format. Sarah Chalke confirmed her involvement in season 9 on June 8, 2009 on Fox News Channel's Fox & Friends talk show.[60] On May 23, 2009, Zach Braff confirmed to Scrubs fans on MySpace his involvement with season 9, but stated that he knew very little about the shape the show will take.[61] Also, Donald Faison, John C. McGinley and Neil Flynn are signed to be regulars for the next season, in second position to other projects.[62] Judy Reyes, according to reports, has not yet been officially approached; however, it is expected that, if she were to reprise her role, it would be merely as a guest star.[63]

On June 19, 2009, it was announced that the reformatted ninth season of Scrubs would "shift from the hospital to the classroom and make med-school professors of John C. McGinley's Dr. Cox and Donald Faison's Turk." According to Lawrence, the ninth season will "be a lot like Paper Chase as a comedy", with Cox's and Turk's students occasionally rotating through the halls of Sacred Heart and encountering former series regulars. McGinley and Faison will be joined by "a quartet of newbies (most of them playing students)" as full-time regulars, while one of the freshmen "will be fairly famous".[64]

The biggest change to the show on the upcoming season is a major cast revamp. Of the seven actors who have appeared in the show since the pilot, only Donald Faison and John C. McGinley are returning in regular roles. Zach Braff and Sarah Chalke are set to reprise their roles as J.D. and Elliot respectively for the first six episodes of the season[64] Neil Flynn will return for the first episode.[4] Ken Jenkins will also return[4][65] and will appear in, at least, the first two episodes[66][67]. The new main cast as it stands so far includes Eliza Coupe[68] returning to the recurring role of Denise "Jo" Mahoney from season eight, Dave Franco as Cole, a charming, conservative, confidently stupid and incredibly entitled medical student whose family donated a wing to the school,[69] Kerry Bishé will play Lucy, the new narrator for the show,[4][70] and Michael Mosley has been announced as playing Drew, a 30-year old med student on his last attempt at school.[70][71] Former Gilmore Girls star Lauren Graham was rumored to be "at the top of [ABC's] wish-list" of potential big-name actors.[72]

Another major change will be the setting of the show and where it is filmed. For the first eight seasons, the show was filmed at the North Hollywood Medical Center but production for this season will take place at Culver Studios. As a result, in the show, the existing Sacred Heart hospital will be mentioned to have been torn down and has been partially re-built on campus - due to the economy they ran out of money while building the hospital and construction ended. There will be "doors that go to nowhere and half-finished operating rooms".[4]

On October 28, 2009, it was announced that season nine will premiere on December 1, 2009 with back-to-back episodes