Baer was hired by writer and producer John Wells to write for drama series China Beach. The series focused on nurses in Vietnam and Baer was nominated for a Writers Guild of America Award for Best Screenplay in Episodic Drama his work on the episode "Warriors". During this time, Baer prepared a film script treatment for Paramount called The Lost Mariner, based on a story from the book The Man Who Mistook His Wife for a Hat by Oliver Sacks, but the project was not produced.
Baer was hired by John Wells again as a staff writer for the first season of ER. He contributed directly to four episodes and his medical experience informed other storylines. He became a story editor for the second season, taking responsibility for compiling scripts and developing the medical storylines. As a story editor, Baer worked alongside fellow medical professional Lance Gentile. Baer remained a regular writer and contributed scripts for the episodes "Hell and High Water" and "The Match". Baer and Gentile were promoted to executive story editors by the end of the season. Baer was nominated for an Emmy Award for Outstanding Writing for a Drama Series at the 1996 awards for his work on "Hell and High Water".
Baer became a co-producer on the third season of ER and wrote a further four episodes. The third season was nominated for a Primetime Emmy Award for Outstanding Drama Series at the 1997 awards. The producers shared the nomination for their work on the season. Baer was personally nominated for a second Emmy Award for Outstanding Writing for a Drama Series for his work on the episode "Whose Appy Now?". He was also nominated a second Writers Guild of America award for Best Screenplay in Episodic Drama for the same episode in at the 1998 ceremony.
Baer was promoted to producer for the fourth season and wrote two more episodes. The season was again nominated for the Emmy Award for Outstanding Drama Series at the 1998 awards and Baer shared the nomination forĀ aĀ second time.
Baer was promoted again to supervising producer for the fifth season. He was responsible for writing a two more episodes, continuing to develop medical storylines for all episodes, and supervising other aspects of production including casting, design, directing, and editing. Baer was also responsible for answering mail relating to the medical aspects of the series and for developing projects that drew on ER to promote public health including a series of news segments covering issues related to the series. The fifth season was also nominated for the Emmy Award for Outstanding Drama Series at the 1999 awards and Baer shared the nomination forĀ aĀ third time.
Baer became a co-executive producer for the sixth season of ER and wrote a further three episodes. The sixth season was also nominated for the Emmy Award for Outstanding Drama Series at the 2000 awards and Baer shared the nomination forĀ aĀ fourth time.
Baer was promoted to executive producer for the seventh season of ER and wrote one more episode. The seventh season was also nominated for the Emmy Award for Outstanding Drama Series at the 2001 awards, marking Baer's fifth consecutive nomination for the award. Baer left ER following the seventh season,Ā havingĀ been a producer for five seasons and with 18 episodes as a writer.
Following his departure from ER, Baer became executive producer and showrunner for Law & Order: Special Victims Unit from the second season until departing afterĀ 12th seasonĀ to move to CBS Television Studios.
Baer has written the pilot episode of two unproduced television series; The Edge for CBS and Outreach for the WB Network. Baer served as a writer and producer for the pilot of Outreach and the episode aired on A&E in 1999, but the series was not picked up. Baer has also written an unproduced film for Twentieth Century Fox entitled The Doctor Corps. Baer is a trustee of the Writers Guild of America Health and Pension Fund.
From 2013-2015, he served as showrunner and executive producer of the TV series Under the Dome. In 2015, he co-wroteĀ alongĀ Marc Cherry and Dan Truly the pilot episode of the comedy crime series Cheerleader Death Squad.
Fox has purchased Baer's show The Beast for the 2017-2018 season. The show, to be written by Baer and Dawn DeNoon and produced by 20th Century Fox Television in association with Baer Bones, will be a medical drama in which the main character has a clinical fear of death.
