The mission of the Emerald Coast Science Center is to inspire exploration, discovery, and interest in science through interactive exhibits and the highest quality educational programs.

In the late 1980s, the Jr. League of the Emerald Coast led by Dr. Alexis Tibbetts began a feasibility study to see if Okaloosa County could support a science museum. The response was overwhelming and with the support of the city of Fort Walton Beach, Okaloosa County School System, the University of West Florida, Okaloosa Walton Community College, local business owners and government contractors, the plan to build a science museum in Fort Walton Beach was put into action. In 1989, the Emerald Coast Science Center opened its doors as the FOCUS (Families of Okaloosa County Understanding Science) Center. The name FOCUS emphasized the priority of the founders that the center was not just for children or adults but it was a center for families to learn about science together.

Initially the FOCUS Center was a volunteer run organization run by the members of the Jr. League. Exhibits were made by local businesses and volunteers with an emphasis on hands-on learning. It was open to the public on the weekends and was a field trip destination for Okaloosa County students during the week. As the popularity of the FOCUS Center grew, it became apparent that the organization was becoming an entity that required more staff and more funds so in 1992 it was decided to allow the organization to incorporate as a not for profit 501(c)(3) corporation. During the next 9 years, the FOCUS Center worked intimately with the Okaloosa County School System to provide lab-based activities at the center as well as at the local schools.

In 2001, the FOCUS Center changed its name to the Emerald Coast Science Center (ECSC) to better promote the museum as a regional science museum for Northwest Florida. Beginning in 2001 the museum expanded its operating hours to seven days per week and purchased professionally designed exhibits. It also began offering more on-site programs including scouting workshops, weekend discovery programs, after-school programs and evening programs as well as teacher professional development classes.