The first school in the Wayzata area was established in approximately 1855. Records are spotty, but indications are that classes were taught in homes until a one-room log school was built near what is now the second green of the Wayzata Country Club. This school mysteriously burned down and a new school was constructed on what is now the main street of Wayzata.

In 1870, the taxpayers voted $900 in bonds to build a new school on Bald Hill – the site of the former Widsten School and the current Wayzata City Hall. That school was replaced in 1880 by a magnificent red brick structure that featured folding doors between two rooms - a forerunner of the open school concept.

By 1903, Wayzata had established a four-year high school and in 1906 graduated its first class of three students.

By 1910, the 30-year-old school that had been the pride of the community was dismantled and a new structure built. Unfortunately, a few years later this school also burned down. It was replaced in 1922 by a building with architecture that resembled a Mexican hacienda. This building was known as Widsten School and served students until the building was closed in October 1989. The students and staff from the school were reassigned to Gleason Lake Elementary School.

The Beacon Heights/Medicine Lake area consolidated with Wayzata Public Schools in 1946 and resulted in the acquisition of the district's second school - Beacon Heights Elementary School. Beacon Heights continued to serve the district until it was closed in 1982.

In 1951, the new Wayzata Junior/Senior High School opened. This building housed all students in grades seven through 12 until it became a junior high school (now West Middle School) with the opening of Wayzata Senior High School in 1961.

In 1956, five one-room school districts in the northern part of the district consolidated with Wayzata Public Schools. These land acquisitions resulted in the present configuration of the district of approximately 38 square miles. New elementary schools were opened in 1958 (Oakwood), 1963 (Sunset Hill), and 1965 (Greenwood). 

When it initially opened in 1967, Ridgemount Junior High School housed grades 7 through 9 until it was renamed Wayzata East Junior High in the mid-1980s. It converted to Wayzata East Middle School in 1997 after the construction of the current high school.

The next construction occurred when Birchview Elementary School was built in 1970.

Plymouth Creek Elementary and Gleason Lake Elementary Schools opened in 1989. Kimberly Lane Elementary School opened in 1991.

The current Wayzata High School, serving students in grades 9 through 12, opened in the fall 1997. The high school building that opened in 1961 was converted into Central Middle School in 1997.

Due to a growing resident student population, voters approved building Meadow Ridge Elementary School, the district's eighth elementary school, which opened in the fall of 2016. A 10-classroom addition opened in the fall of 2018 to accommodate additional growth.

Resident student growth remained robust. Voters approved building a ninth elementary school, North Woods, in November 2017 that opened in the fall of 2019.

With enrollment continuing to increase, an addition to Oakwood Elementary was completed in the Fall of 2020. The addition included more classroom space and a new gymnasium. The addition to Oakwood also includes space for the Wayzata Early Learning School and a new Education Services Center.