Because of drainage problems and settlement of the second set of timbers the Winston Tunnel had to be extensively rebuilt only fourteen years after it was originally completed. The contract was awarded to Lorimer, Gallagher, & Walsh Construction Company to reline the tunnel with brick and concrete and rebuild the floor and approaches. In 1902 construction began and would continue day and night for two years.
The approach to the east portal was rebuilt in connection with the tunnel work. A 24 inch tile drain was set in concrete and extended from the east portal to the end of a 1000-foot cut designed to divert ground water away from the tunnel. Heavy masonry retaining walls were built on both sides of the long cut.
Because of limited workspace in the tunnel, work on the arch had to be done from scaffolding added to cars that also contained the workers and the material. The only material not on the cars was the material that was added to the tunnel. Mortar was mixed on the floor of the cars and passed up through trap doors; bricks were also tossed up from the floor of the cars.
The Tunnel was part of the system's busiest main line, 25 scheduled trains passed through it daily, keeping work trains running day and night. About 15,000 barrels of cement, 2,500,000 bricks, and 11,000 cubic yards of gravel were needed. Construction was completed without a serious accident.