From February, 1889, to May, 1892, Thayer was out of railway work before returning to the PRR in May, 1892, as division freight agent of the Northern Central, with headquarters at Baltimore, MD. On December 1, 1894, he was promoted to assistant general freight agent, with office at Philadelphia, Pa., and in March, 1897, was made general freight agent in charge of through traffic. In May 1899, he was appointed general freight agent also of the Northern Central, the Philadelphia, Wilmington & Baltimore, and the West Jersey & Seashore. Thayer was elected fifth vice-president, in charge of traffic of the Pennsylvania Railroad on June 1, 1903.