Bedford Township was formed in 1767 within Cumberland County. Frankstown Township was formed in 1775 out of the northern third of Bedford Township and the western half of Barre Township. Woodberry Township was then formed out of the southern third of Frankstown Township in 1785. The part of Woodberry Township that lay west of Dunnings Mountain was removed in 1798 to form Greenfield Township. In the meantime, in 1794, St. Clair Township had been formed from a portion of Bedford Township; its eastern boundary with Bedford Township lay along the summit of Wills Mountain in the south and Dunnings Mountain in the north. A portion of the northern part of St. Clair Township was removed in 1834 to form Union Township along with a portion of Greenfield Township that had been formed out of Woodberry Township.
St. Clair Township was further reduced in size by the formation of Napier Township out of its southern half. Napier Township was formed in the year 1811 out of St. Clair and a portion of Bedford Township. Napier was later reduced in size when Harrison was formed out of it in 1840. Juniata Township was then formed out of portions of Harrison and Napier Townships in 1853. When St. Clair Township was formed out of a portion of Bedford Township in 1794 the division line between the two was the so-called Great Road.
Napier Township was named in honor of Lord John Napier. John Napier (1550 to 1617), was the 8th Laird of Merchiston, a residential area of southwest Edinburgh, Scotland. He was best known as the inventor of logarithms and an early advocate of the use of the decimal point in mathematics. In fact, he was very accomplished in many fields and authored a number of books on theology. Sir Charles James Napier, 1782 to 1853, was a general during the Peninsular War that lasted from 1807 to 1814 in which Great Britain, Spain and Portugal battled Napoleons French army for control of the Iberian Peninsula. General Charles James Napier was suggested by William P. Schell in an article published in the 04 February 1898 issue of the Bedford Gazette. The entry that was recorded in Road Docket #1 clearly noted that the new township was "Called Napier in honour of Lord Napier, the inventor of Logarithms by which Mathematical calculation has been shortened.
Although the township is relatively young, its name having been bestowed upon it as recent as 1811, the use of its land is ancient.
The earliest habitation by humans within the bounds of Napier Township would have been the Amerindian village of Shawana Cabins (variously, Shawnee Cabins). The Shawnee Amerindians, members of the Algonquian language group, were also known as the Shawanese. Located about one and one-half miles east of the present-day borough of Schellsburg, the collection of huts known by the Euro~Americans as the Shawana Cabins probably served as a seasonal migration stop-over camp rather than a village in which the Amerindians lived year round. The Shawana Cabins were noted in the 1884 History of Bedford, Somerset and Fulton Cos., Pennsylvania as being located at that time on the C. W. Colvin farm. At this present time that site would be in the Shawnee State Park and possibly underneath the Shawnee Lake.