After leaving the Illinois Central and undergoing heart surgery, Moyers was asked to return to railroad service by Philip Anschutz, the executive behind the Rio Grande Railroad's purchase of Southern Pacific Railroad (SP). Moyers became chairman and CEO of Southern Pacific Company (the parent company of Southern Pacific Railroad) and president of Southern Pacific Railroad in July 1993, leading the railroad up to the merger of Southern Pacific into Union Pacific Railroad. Part of his leadership strategy at SP, like his strategy at Illinois Central, was to trim excess capacity, such as by single-tracking sections of SP's Donner Pass line. Moyers also questioned the efficiency of the former Rio Grande's Tennessee Pass line versus its Moffat Tunnel line; he noted that the steep grades of Tennessee Pass led to increased fuel and maintenance costs to the railroad, favoring the shorter and lower elevation Moffat route. Under Moyers' leadership, SP went from a $149 million loss in 1993 to earning $242 million in 1994. The Southern Pacific Company announced on February 8, 1995, that Moyers had submitted his resignation, citing advice from his physicians. Southern Pacific was acquired by Union Pacific in 1996.