Walnut Heights School opened in 1951, with the Walnut Heights PTA founded in November of that year. Dr. Elmo Giulieri, past Superintendent of Schools, was the first principal. He was succeeded for two years in 1953-55 by Floyd Buchanan, followed by Dr. Lloyd Scott during the 1955-57 school years.

Alden MacKay took over as principal in 1957 and was succeeded in 1961 by Bob Henry, who served for sixteen years. During that time, the Nature Area was established in 1968, and improvements were made to the school's recreation facilities and the library. Earl Allen served as principal from 1977 to 1986. Upon his retirement, Nancy Rivara - who had been Vice Principal at WCI - was named his successor.

From 1994 to 2007,  Diane Collen was principal.  Ms. Collen was a former Parkmead Elementary School principal and Walnut Heights parent. That same year, upon the retirement of Dr. Ken Meinecke, Walnut Heights was introduced to its new Walnut Creek School District Superintendent, Michael De Sa.

Major changes during the 1996-97 school year included the resurfacing of the roof, a new configuration of the parking lot, and the rapid implementation of class size reduction in Grades 1 - 3. The following year, Kindergarten classes also were limited to 20 students.

Massive modernization and renovation began in the summer of 1997, including white boards, air-conditioning, and wiring all classrooms for technology. In 1998 a new kindergarten area, upgraded offices, and a new Library Media Center were completed. These improvements were carried out using monies available from a bond measure which was passed several years before.

Over the years, many changes have taken place in the school facilities and surrounding neighborhoods. Remaining constant is a continued effort toward achieving high academic standards, and the exceptional level of family involvement and community spirit at Walnut Heights.

In 2007, Susan Drews became principal of Walnut Heights.