Much of the original equipment came from the Utah & Northern Railway in Idaho and Montana. The Union Pacific owned the line and began converting it to standard gauge around 1887. Eccles owned a significant amount of Union Pacific stock, exerting enough influence to acquire the now-unneeded narrow gauge equipment. The first locomotive to arrive was a small 4-4-0 numbered 285; the Sumpter Valley also purchased a number of the U&N's Brooks 2-6-0 locomotives, along with a large number of boxcars and flatcars. In 1906, the railroad also acquired four locomotives from the Tonopah Railway (later the Tonopah & Goldfield Railroad).
By 1891, the line had reached McEwen, 22 miles (35 km) west of Baker City, and the railroad began offering passenger and freight service. To reach uncut forests further west, the company extended the line in stages. It reached Sumpter in 1896 and continued southwestward to Whitney, Tipton, Austin and Bates. By 1910, it arrived in Prairie City, a ranching and mining community along the John Day River in Grant County. The railroad continued to use wood fuel for their locomotives until converting to oil fuel in June, 1940. Diamond-shaped smokestacks were replaced by cabbage-shaped Rushton stacks after 1916.
Ten years later, the railway began losing business to automobiles and trucks, and in 1933 the 20 miles (32 km) of track between Prairie City and Bates were abandoned. Scheduled passenger service on the remaining line ended in 1937. Freight service remained, however, and in 1939 the railway purchased two 2-6-6-2T "mallet" locomotives from the Uintah Railway in Colorado. These engines were converted from coal to oil burners and given tenders from two 2-8-2 locomotives. As traffic declined, the railway sold off the other, unneeded locomotives. In 1947, the railroad ceased all operations except for 1.5 miles (2.4 km) of track in the Oregon Lumber Company yard in South Baker City. This last section was abandoned and removed in 1961.