After the war, Baxter remained in the Army as a member of the newly-organized Medical Department, and was appointed Assistant Medical Purveyor with the rank of lieutenant colonel. In 1872, he was appointed Chief Medical Purveyor, and in 1874 he received promotion to colonel. In 1875, Baxter graduated from Columbian University (now George Washington University Law School) with an LL.B. degree. Baxter's duties as Chief Medical Purveyor included serving as personal physician to the President of the United States, and he attended James A. Garfield's family. Baxter was out of town when Charles J. Guiteau shot Garfield in July 1881, and was not able to examine Garfield following the shooting. Garfield's other physicians prevented Baxter from seeing Garfield, which generated controversy both immediately after the shooting and after Garfield's death several weeks later.