The Milroy Secondary has a rather convoluted divisional heritage.

Lewistown Division

In 1896, the Mifflin & Centre County Railroad merged with the nearby Sunbury & Lewistown Railroad. The PRR executed a new 79 year operating lease on October 1, 1896. It was operated as the Lewistown Division.

The 1900 edition of the CT1000 lists the Milroy line under the Lewistown Division.

June 1, 1900 North & West Branch Railway, Pennsylvania Schuylkill Valley Railroad, Sunbury, Hazleton & Wilkes Barre Railway, and Sunbury & Lewistown Railway merged to form Schuylkill & Juniata Railroad under agreement of Apr. 2, 1900.

Apr. 1, 1902 Schuylkill & Juniata Railroad merged into PRR under agreement of Nov. 27, 1901. The newly absorbed line was detached for operating purposes from the Pennsylvania Railroad Grand Division and became part of the Philadelphia and Erie Grand Division. 

Apr. 1, 1907 Divisional reorganization... Lewistown Division merged with Sunbury Division to form Sunbury & Lewistown Division (also given common officers with Shamokin Division).

Sunbury & Lewistown Division

Mar. 24, 1909 Sunbury & Lewistown Division renamed Sunbury Division.

Sunbury Division

The 1909 Sunbury-Shamokin Division  employee timetable #47, effective May 30, 1909, embeds the line in the station listings under the heading "Selinsgrove Junction to Lewistown Junction" (Lin Bongaardt).

The 1913 Sunbury Division employee timetable includes the Milroy line (George Pierson).

The 1916 Sunbury Division  employee timetable #10, effective June 25, 1916, embeds the line in the station listings under the heading "Sunbury to Lewistown Junction" (Lin Bongaardt).

The 1920 Sunbury Division  employee timetable #1, effective May 23, 1920, embeds the line in the station listings under the heading "Sunbury to Lewistown" (Lin Bongaardt).

The 1921 Sunbury Division employee timetable includes the Milroy line (George Pierson).

A 1922 Sunbury Division track chart, with revisions through 1924, includes the Milroy line.

The 1923 edition of the CT1000 includes the Milroy line under the Sunbury Division listings.

The 1925 Sunbury Division  employee timetable #1, effective April 26, 1925, embeds the line in the station listings under a headingless section spanning Sunbury to Lewistown (Lin Bongaardt).

The 1927 Sunbury Division  employee timetable #6, effective September 25, 1927, no longer includes the line in the station listings. Under a headingless section spanning Sunbury to Lewistown, there is a break at MY Tower. MY Tower, Chestnut Street, Main Street, and Lewistown are included in the Sunbury Division listings (Lin Bongaardt).

Middle Division

Sometime between September 26, 1926, and September 25, 1927, the Milroy line was moved from the Sunbury Division to the Middle Division.

The 1926 Middle Division employee timetable #4, effective September 26, 1926, does not include the Milroy line.

The 1927 Middle Division employee timetable #6, effective September 25, 1927, includes the "Lewistown and Milroy Branches" in the station listings.

The 1927 division accounting maps place the Milroy Branch in the Middle Division.

While the 1932 volume  of Chris Baer's "Chronology of the Pennsylvania Railroad" states that on May 16, 1932 "Schuylkill and Sunbury Divisions merged to form Wilkes-Barre Division with headquarters at Sunbury; Lewistown-Milroy ceded from Sunbury Division to Middle Division", this is apparently in error, given the vast documentation indicating otherwise.

The 1941 division accounting maps place the Milroy Branch in the Middle Division.

The 1942 Middle Division employee timetable #3, effective December 6, 1942, includes the line in the station listings, from Lewistown through Milroy collectively as "Lewistown & Milroy Branches". (Dave Evans)

The 1943 Middle Division employee timetable #4, effective November 14, 1943, includes the line in the station listings, from Lewistown through Milroy collectively as "Lewistown & Milroy Branches".

The 1944 Middle Division employee timetable #5, effective September 24, 1944, drops the station listings, but shows "Lewistown to Milroy" in Special Instruction #2204, "Secondary Tracks of No Assigned Direction" (page 51). It appears that the portion of the Lewistown Branch (Sec. Track) that was in Middle Division was just a short piece east of the junction with the Milroy Branch (Sec. Track). (Lin Bongaardt) 

The 1945 Middle Division employee timetable #6, effective September 16, 1945, shows the Milroy Secondary only in Special Instruction #2204A titled "Other Secondary Tracks of No Assigned Direction" (page 51); this listing is in a station list format (I don't recall ever seeing such a listing in a secondary track Special Instruction.) (Lin Bongaardt) The order refers to traffic between Lewistown and Milroy and does not refer to the track by name; there are no station listings in the front of the document.

The 1945 CT1000 includes the branch in the Middle Division.

The 1946 Middle Division employee timetable #7, effective April 28, 1946, indicates the Milroy Secondary listed in Special Instruction #2204 (Lin Bongaardt). Once again, the order refers to traffic between Lewistown and Milroy and does not refer to the track by name; there are no station listings in the front of the document.

The 1948 Middle Division employee timetable #12, effective September 26, 1948, shows the Milroy Secondary on the station listings (page 9) and in Special Instruction #2204 (page 53) (Lin Bongaardt). The station listings span Lewistown to Milroy.

The 1949 Middle Division employee timetable #13, effective April 26, 1949, still shows the Milroy Secondary on the station listings (page 9) and in Special Instruction #2204 (page 53). The station listings span Lewistown to Milroy.

Until this time, the Milroy line was considered "as built" and spanned Lewistown through Milroy. The Sunbury & Lewistown Railway spanned from MY Tower on the Milroy line to Sunbury. Sometime between April 26, 1949 and April 30, 1950, the S&L became known as the Lewistown Secondary and included the segment from Lewistown through MY Tower. The Lewistown Secondary runs from Lewistown to SAL where it meets the new Susquehanna Division. Subsequently, the Milroy Secondary spanned MY Tower through Milroy. 

The 1950 Middle Division employee timetable #15, effective April 30, 1950, shows both the Milroy Secondary and the Lewistown Secondary tracks separately in the station pages (page 9). They are also shown in Special Instruction #1151-D1 (page 57). It appears that the Lewistown Secondary was transferred to the Middle Division around the time that the Susquehanna Division was formed about late 1949 (Lin Bongaardt).

Pittsburgh Region & Pittsburgh Division

In 1956 the Middle Division would be consolidated into the Pittsburgh Region.

In 1964 this would become the Pittsburgh Division, where it would remain through the end of Pennsy.

During the Conrail years the line would be sold off to the North Shore Railroad System and would operate as the Juniata Valley Railroad