Archbishop Coleman F. Carroll founded the parish of St. Clare in April 1960. In August of 1961, Fr. John W. Schlinkmann was appointed pastor, and plans were made for the construction of a building that would house the Church and the proposed school. The building was completed in February 1964. The upper floor of the building was designated for classrooms, while the lower floor provided room for a temporary church. St. Clare School opened in August 1964 under the direction of the Sisters of St. Joseph of St. Augustine, Florida. The first principal of the school was Sr. John Kevin, S.S.J. The enrollment for the first year of school was 170 students, and the tuition was 20 dollars a month. St. Clare School graduated its first eighth grade in June 1969 when 34 students received their diplomas from Fr. Schlinkmann.

The present St. Clare Church was completed in the summer of 1969, and the building that served as both Church and school is now used solely as a school. Enrollment rose to 481 students, and Sr. Elizabeth Ann was the fourth principal. In August 1970, St. Clare Parish was split, and two new parishes, St. Paul of the Cross and St. Ignatius Loyola, were created. St. Clare School began to serve the children of the two new parishes, as well as the parish of St. Jude in Tequesta. At the conclusion of the school year 1970-71, the Sisters of St. Joseph withdrew the community of nuns, and from then to the present, St. Clare School faculty consisted of lay personnel only.

In August 1971, Mr. Ernest Rovella became the first lay principal with an enrollment of 548 students. In July 1974, Harold F. Shanz was appointed principal. A remedial reading program was introduced to the school. In 1976, a speech therapy program and a school band program were added, along with a school psychologist. In 1977, the present Parish Hall was completed and continues to be used as the school lunchroom to this day. A library was built in 1978 capable of seating 40 students. The first self-study was completed, and the school was accredited by the Florida Catholic Conference in May 1979. In addition, six acres of land were developed for athletic purposes, and the athletic program grew to 16 different sports teams. St. Clare’s kindergarten was established at the beginning of the 1985-86 school year, and a new library was constructed and completed in early April 1986.

Mr. A. J. Houvouras was appointed principal in 1989. The school embarked on a long-range marketing plan to increase enrollment from the 390 students it had at that time. Enrollment rose steadily over the next five years to over 500 students.

In 1989, the Kindergarten building was expanded and remodeled and today, now contains our Pre-Kindergarten classes. Also in 1989, the school instituted its own on-sight computer lab, which was placed in the Media Center (formerly the Library). Other enhancements to the school, through the 90s and into the 2000s, were a fire alarm and security system, a new intercom system, a new playground, a chapter of the National Junior Honor Society, a school counselor, a 3rd-8th grade Spanish program, a school-endowment trust, two resource teachers, a full-time assistant principal, a clinic supervisor, teacher assistants in grades K-2, a teacher salary scale and a school news broadcast. Recent technological advances in the school include interactive smartboards, projectors, and document cameras in the classrooms.

In June 2016, Mrs. Mrs. Rita Kissel was appointed principal of St. Clare Catholic School. 

In July 2023, Mrs. Rachel Polak was appointed principal of St. Clare Catholic School.  She has deep ties to the community as her husband and children are all alumni of St. Clare Catholic School.