The Milford Branch had originated as a branchline of the Fitchburg Railroad, coming off of the main line at Ayer, Massachusetts and finding its way north into Milford, New Hampshire. The railroad companies that the Fitchburg supported were chartered in 1891 and 1892, and trains were running to Milford by 1893. Originally leasing the lines from the three charter railroads, the Fitchburg formerly acquired them in 1895. Five years later, the Boston &; Maine Railroad took over the Fitchburg.
The Milford Branch followed the opposite bank of the Nashua River up towards Pepperell from the Worcester, Nashua & Portland (WN&P) Division main line. The Pepperell station for the Milford Branch was less than a mile from the one on the W&NP. Passenger service ceased in 1931 and ice, the reason for the construction of the branchline, remained the big customer on the line until 1935. That year a fire ripped through the Brookline ice house and thus started the decline of the branch. Abandonment the line between Milford and Pepperell occurred in 1939, except for a small stretch in Milford that continued to serve an active granite quarry.
With the remaining customers in Pepperell, the Boston & Maine constructed a bridge that spanned the Nashua River north of the town center. A spur off the WN&P main line connected to the Brookline & Pepperell Branch near the Pepperell Paper Co. paper mill north of the branch's Pepperell depot. This enable the Boston & Maine to abandon the redundant track south of town in 1942. The last bit of the Milford Branch remained in service until 1982.
The right of way can be very hard to trace in some locations as the roadbed has grown in considerably. In addition to vegetation, near the Groton-Pepperell town line homes have been built on the roadbed and N.H. Route 13 was constructed on the roadbed in Brookline. All is not lost however, as sections in Pepperell, Hollis, Brookline and Milford have been preserved as rail-trails by either local or state conservation commissions and included in the trail network within the conservation land owned by Beaver Brook Association.