When the Manchester & Lawrence Railroad (M&L) was built in 1848 and 1849, it constructed a small station at the crossing of Depot Road. It was only a few years later when the Nashua & Rochester Railroad (N&R) was constructed in 1873, which crossed the M&L only a couple hundred feet south of the its station. The Nashua & Rochester Railroad constructed a new station a year later at the junction for a cost of $2,200 and the old station was moved away from the railroad tracks. The new station was called Windham Junction. On June 20, 1910, the Boston & Maine Railroad renamed the station to simply Windham.

The junction of the M&L and the N&R was protected by a ball signal. The position of two balls on a tall mast would indicate which rail line had the right of way at the junction. Interestingly enough, a train order signal was only used on the Nashua & Rochester side originally. Heading into the 1900s saw the addition of a train order board for the Manchester & Lawrence.

The last passenger train on the Nashua & Rochester line ran on March 3, 1934 with a gas-electric motorcar. Freight service had ceased on this portion of the line earlier in 1932. The tracks on that line were removed a year later in 1935. Despite the Manchester & Lawrence Branch was still seeing regular passenger service, the station was closed on September 14, 1935. A gas-electric car did a single round trip on the Manchester & Lawrence until July 10, 1953.

Both the original Manchester & Lawrence station and the Windham Junction station built by the Nashua & Rochester Railroad still exist. Since the M&L station was moved, it has been used as a private residence. The Windham Junction station was used by the railroad until ##. Both the passenger station and the freight house were used by the New Hampshire highway department and in more recent history they were used by the Town of Windham as their highway department. Activity has since returned to the junction, with the development of the popular Windham Rail Trail. In 2010 the passenger station and freight house were restored.

Dinsmore, Bradford R. "Windham Junction." In Windham. Charleston, SC. Arcadia Publishing, 2003. 57-68.
Hoisington, Richard A. "Windham... Change for Lawrence and Boston!" B&M Bulletin, Winter 1976-1977.
Hoisington, Richard A. "This Train Does Not Stop at Nutt's Pond." The New England States Limited, Spring 1978.

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