The line was built by lumber baron John Rudolphus Booth, who also built the OA&PS. The line is named for John Egan, the owner of 250 square miles of land in today's Algonquin Provincial Park. Egan had developed the land by opening several "depot farms" that sold produce to the workers in the surrounding areas.
Egan died in 1854, and after lying relatively unused for some time, Booth purchased the 650 square kilometer estate in 1867. He built the current town of Madawaska on the southeast corner of the plot, centralizing development in the area, which had formerly seen only a few plots from settlers travelling into the area on the Opeongo Road. Construction of the OA&PS took place between 1885 and 1896 and the Egan Estates Railway was built sometime during this period. Madawaska became the divisional point for the OA&PS, and a large lumber yard was constructed there.
As the logging areas in the present Algonquin Park were used up, the work focused more on the Madawaska area, and Booth moved to the town. With the abandonment of the Nosbonsing and Nipissing Railway (N&N) in 1912, another of Booth's lumber railways, the N&N charter was used for the Egan Estates, although it was rarely referred to this way.
The Madawaska area was also logged out by the 1920s, which combined with the effects of World War I and the Great Depression, led to a crash in the square log market. The OA&PS ran a train every 15 minutes at its peak, with 4 passenger trains a day, but by 1926 this was down to 1 to 2 trains a week. During the 1930s, much of the Egan Estates line was lifted and shipped out, along with much of the OA&PS infrastructure in Madawaska.