Initial hunters and settlers in the territory that includes present-day Jenner Township were Mingo, also known as the Seneca, one of the Six Nations of the Iroquois.

[5] The land was ceded by the Iroquois Six Nations officially by the Treaty of Fort Stanwix of 1768 to Penn family as proprietors of Pennsylvania province.

The Northern Trail, an established Indian trail, crossed the territory from east to west, intersecting Quemahoning Creek at Kickenapaulin's Town, a rather substantial Indian settlement, the site of which now lies under the waters of the Quemahoning Reservoir, just outside the township.

Early Jenner Township settlers were primarily German and English speakers engaged in agriculture.

[12] Jenner Crossroads, the township's first substantial European settlement, grew near a grist mill and tavern stop established about 1800 along the Pennsylvania Road.

[14] Other early industry in the township included a sawmill on Quemahoning Creek built about 1813 by Moses Fream and a small woolen mill, built in 1817 by William Dalley, enlarged by Owen and William Morgan later into a small settlement known as Morgantown.

Immigrants from Poland, Italy, Russia, Ruthenia, Wales, and Ireland filled the coal towns.

The town of Randolph was also a very small coal mining community in Jenner Township, any trace of which is now virtually gone, having been destroyed by highway construction in 1970.

Jenner Township also serves as a bedroom community for the nearby Somerset and Johnstown areas.

The Bridge in Jenner Township and Matthew Hair Farm are listed on the National Register of Historic Places.