The Stony Brook Railroad was chartered in 1845 by citizens of Lowell, Massachusetts, to connect the city with points south and west.

As the line approached completion, the Stony Brook decided to contract out train operations to the Nashua and Lowell Railroad (N&L), which connected to the line at its eastern terminus in North Chelmsford, rather than purchasing and operating their own trains.

Under the B&M, the line grew in importance as a route for traffic between Maine and the rest of the United States which bypassed the busy city of Boston.

A wye was constructed in 1930 at North Chelmsford, which allowed trains traveling to or from Nashua, New Hampshire, to use the line without having to make a reverse movement.

In April 1946, the B&M built a connection between the two lines at Willows, allowing for the duplicate trackage to Ayer Junction to be abandoned.

[3] On May 24, 1911, a circus train carrying Buffalo Bill's Wild West show derailed on the Stony Brook Railroad near Brookside.

The accident, described by The Boston Globe as "one of the most spectacular in the history of railroading in this section," was later reported to have been caused by a ramp for loading and unloading elephants.