The San Luis Rey spur branched from the Fallbrook Branch, also abandoned, at Oceanside and headed inland to serve Mission San Luis Rey de Francia, in the tiny community of San Luis Rey. Built in 1913, the spur followed the San Luis Rey river and ran for 4 miles to reach the mission. The branch line also served a sugar beet/grain warehouse, as well as including short spur at the city pumping plant for the delivery of fuel oil and supplies.

The San Luis Rey River flooded in January of 1916, washing out much of the right-of-way along with the railroad's bridge at the mouth of the river.

From the Blade Tribune, dated 8/25/1917: A communication was received from the State Railroad Commission notifying the board of the application of the Santa Fe "for authority to abandon permanently a spur track known as the San Luis Rey Branch, extending from San Luis Rey Junction to San Luis Rey in the County of San Diego," it being alleged that it is a physical impossibility to maintain the spur track in its former location, that the line has not been operated since the floods of the early part of the year 1916 and that the earnings from this spur track did not justify its reconstruction and operation.