The present school board has five nonpartisan members who are elected by popular vote and are limited to a four-year term.

Hayesville Primary covers Pre-K thru 2nd grade and has an enrollment of approximately 372 students.

The current two-story brick facility on the east end of campus was constructed in 1991.

[6] In the 1850s, one-room log cabin pay schools opened in Tusquittee, operated by John Oliver Hicks.

After Hicks was elected as the first representative from Clay County to the North Carolina General Assembly, he purchased land near Hayesville on Aug. 12, 1870, to establish a school, Hicksville Academy.

Hicksville Academy boarded students and charged tuition in a framed, two-story building.

[7] The Hayesville Colored School was located at the old Mauldin Place near the present day landfill on Hinton Center Rd.

[9] In 1898, the college changed ownership and, after the state required counties to stop charging for education, elementary courses were offered for free at Hayesville Graded School.

[7] The county had as many as 18 public schools operating in the early 1900s, most of them one-room schoolhouses that provided instruction through only the seventh grade.

[7][11] The brick schoolhouse was the first school in the county to feature indoor plumbing and running water, which was supplied by an on-campus well.

[9] Hayesville High School stopped charging tuition in 1928 and fielded a football team in 1929.

[13] The system further consolidated from eleven schools to four, with Hayesville, Ogden, Elf, and Shooting Creek remaining.

As schools were still racially segregated, Clay County’s African-American students were bussed daily to Murphy, North Carolina on a pickup truck to attend an all-black school in the Texana community.

Other closings included Upper Tusquittee in 1941, Oak View in 1946, Fires Creek in 1948, and Sweetwater in 1948.

Most consolidations were welcomed as they provided students an opportunity to attend high school.

[7] Hayesville's sports teams adopted the "Yellow Jackets" moniker and mascot by the 1970s.

In the 1970s, students in the high school carpentry-masonry class built homes which were sold and also constructed the Clay County jail.

The house was the former Base Penland homestead, moved around 1941 from the Elf community to Hayesville to spare it from flooding during the creation of Chatuge Lake.

In May 2022, Clay County Schools announced plans for a new structure that will house grades 3-8; a new gym for Hayesville Middle School; a cafeteria to serve grades 3-12 and a new performing arts center.

[14] The project broke ground in July 2024 and the campus auditorium was demolished shortly thereafter to make room.

[15] Starting with the 2024-2025 academic year, all Clay County Schools students were provided with free breakfast and lunch due to a federal grant established by the Healthy, Hunger-Free Kids Act of 2010.