Pendleton Heights was built in 1969 as a consolidation of Adams Township's Markleville High School and FallCreek Township's Pendleton High School. The consolidation happened after the Indiana State Legislature passed the School Reorganization Act, causing the redistricting of school boundaries so that each student was backed by $5,000 in assessed tax evaluation. Under this Act, Markleville High school no longer qualified as a public high school. In 1959, a nine-man school reorganization committee was appointed to redistrict the school systems of Madison County.

After much discussion and many public meetings throughout the county a plan was devised that met all requirements. In southern Madison County the new school district consisted of Green, Fall Creek and Adams Townships. The area chosen to build the new consolidated school consisted of approximately 112 acres (0.45 km²) just east of Pendleton, bordering State Road 67 andState Road 38. Central location of this site to the schools was considered in the selection. The property was sold to the school in early 1967 with construction on the new high school starting in October of that year. The original building was completed for occupancy September 1, 1969. At the time the new Pendleton Heights was a state of the art, one of a kind public high school in central Indiana with the first graduating class in 1970.

In 1996 the school began construction with a remodeling and renovation project. The project; which consisted of a new academic wing and media center, a 900 seat auditorium and performing arts center, and an auxiliary gymnasium; was completed in Spring 1999. In Spring 2009, the 10 year anniversary of the renovation was celebrated with the "Loran G. Skinner's 10th Anniversary Gala", which featured the High School's Pendletones show choir, the PHHS Jazz Band, and revival performances of plays and musicals by previous cast members.