Upon graduating law school in 1975, Baer took a job with the Federal Trade Commission where he held positions as Assistant General Counsel and Director of Congressional Relations; Attorney Advisor to the Chairman; Assistant to the Director, Bureau of Consumer Protection; and Trial Attorney, Bureau of Consumer Protection. Baer left the FTC in 1980 to join the law firm Arnold & Porter. He was an associate at the firm from 1980 until 1984, when he became a partner. He remained a partner at Arnold & Porter until 1995, and among his higher-profile cases was successfully defending General Electric against price-fixing accusations in the 1990s. In 1995, Baer left Arnold & Porter to rejoin the FTC as the director of its Bureau of Competition. Baer left the FTC in October 1999. In January 2000, Baer returned to Arnold & Porter as a partner. In his practice, he represented a broad range of firms in U.S. and cartel investigations, mergers and acquisitions reviews, and antitrust litigation. Baer held that role until his retirement in 2012. Per his disclosure when joining the U.S. Department of Justice in 2012 Baer continues to receive payments from Arnold & Porter until 2025 as part of his retirement package. In 2012 Baer became assistant attorney general for the antitrust division in the Justice Department.
On February 6, 2012, President Obama nominated Baer to serve as Assistant Attorney General for the Antitrust Division, filling the slot vacated by Christine A. Varney. During his hearings before the United States Senate Committee on the Judiciary in July 2012, Baer told senators that he felt that the Antitrust Division had been "well run in recent years." However, his nomination stalled in the second half of 2012 after some Republican senators said they did not like something discovered in Baer's background check. On September 20, 2012, Baer's nomination was voted out of committee to the full U.S. Senate in a 12–5 vote. On December 30, 2012, the full U.S. Senate confirmed Baer in a 64–26 vote, with all votes against him coming from Republicans. The first case for Baer to oversee in June 2013 was a trial that the Division filed accusing book publishers of conspiring with Appleto fix the prices of e-books. The Justice Department contends that since the trial, the average price of best-selling e-books has dropped to about $6 from $12.99 before. On March 1, 2016 Baer filed an Antitrust Division indictment against oilman Aubrey McClendon alleging conspiracy to fix bidding on freehold oil and natural gas leases. The following day McClendon drove his vehicle at high speed into a bridge embankment in Oklahoma City and died instantly in what the police ruled an accidental death. On March 3, 2016 the Justice Department withdrew the charges.
