On December 20, 1901, Garrett was appointed customs collector of El Paso, Texas by Theodore Roosevelt. Garrett served for five years in this position, however he was not reappointed. This was possibly because he had embarrassed Roosevelt by showing up at a San Antonio Rough Riders reunion with a notorious gambler friend named Tom Powers. That resulted in a bit of bad press for Roosevelt because Powers had been run out of his home state of Wisconsin for beating his father into a coma. Garrett retired to his New Mexico ranch but had a great deal of money problems, including owing a large amount in back taxes.
Garrett would eventually be forced to sell his ranch to pay these debts and would enter into negotiations with a man named Adamson for the sale. He and Adamson were riding from Las Cruces in Adamson's wagon when they were approached by Jesse Wayne Brazel (who was renting land owned by Garrett). Garrett and Brazel began to argue about the goats grazing on this land and Garrett allegedly leaned forward to pick up a shotgun on the floorboard. Brazel shot him once in the head, and then once more in the stomach as Garrett fell from the wagon. Brazel and Adamson left the body by the side of the road and returned to Las Cruces, alerting Sheriff Felipe Lucero of the killing. Brazel claimed the shooting was in self-defense and Adamson backed up his story.
Garrett's body was too tall for any pre-made coffins available, so a custom one had to be shipped in from El Paso. His funeral service was held March 5, 1908. His body is interred at the Las Cruces Masonic Cemetery, Dona Ana County, New Mexico. Garrett's death is now commemorated by a historical marker, which can be visited off of the south of U.S. Route 70, between Las Cruces and the San Augustin Pass. The highway marker is not at the actual spot where Garrett was shot. Pat's son Jarvis Garrett marked the location of the shooting in 1938-1940 with a monument of his construction. The monument consists of cement laid around a stone with a cross carved in it. It is believed that the cross is the work of Pat's mother. Scratched in the cement are "P. Garrett" and the date of his killing.