Primarily located in unincorporated St. Johns County, Florida (with a St. Augustine address),[2] the organization offers "Centers of Excellence" in bariatrics, heart, cancer, maternity, orthopedics and sinus.

Dr. Sloggett purchased a house on Marine Street for his home in 1884, but his goal was to eventually transform the structure into a hospital.

[5] The children of the St. Augustine Loyal Temperance held a fair at the Union chapel on April 7, 1888.

On May 22, 1888 he invited St. Augustine's most influential women to his Ponce de León Hotel and offered them a hospital if the community would commit to operate and manage the facility.

To meet the increasing demand for healthcare, the hospital's south wing was renovated, providing room for a clinic and doctor offices.

The hospital was expanded to provide more surgical capacity and an in-house psychiatric services center was established to serve the area.

Planning began for a new health park on a more accessible 75-acre parcel along the east side of U.S. Highway 1.

[9] Two years later, Flagler merged with St. Augustine General Hospital, doubling the number of patient beds from 150 to over 300.

[citation needed] In November 2005, Flagler sold its Community Home Health unit, which provides home visits by a nurse, to Almost Family, Inc.[10] Prior to the Great Recession, the hospital announced plans to build a $30 million medical park at the World Commerce Center.

[14] In 2021, Flagler Health+ purchased land in northern St. Johns County and Palm Coast to develop new hospitals.

[18][4] The hospital has a 14-bed nursing home unit that was rated above average on October 5, 2010 from CMS of the Department of Health and Human Services.

[19] Flagler has centers of excellence in Imaging, Bariatrics, Cancer, Heart, Spine, Maternity, Orthopedics and Sinus.