The Trees for Health arboretum began as a project of the San Diego Herb Club in 1993 to identify and map medicinally useful trees in Balboa Park and then plant 15 more. The original founders were Barbara Carey, Fern Wilson, and Charlotte Tenney.

In 1995 the project expanded when the Balboa Park horticulturist arranged for Trees for Health to have a permanent space, at the corner of Quince Drive and Balboa Drive. Working with the park nursery, the Herb Club team planted 35 trees by the end of 1995. The project has continued to grow since then. In 1998, the garden space was expanded to cover 3 ½ acres, and more trees were planted. Currently there are over 70 trees along with shrubs and ground cover, all with medicinal value.

The plants are now an established collection, maintained by a dedicated crew of volunteers. Paths were resurfaced and seating areas were added in 2013 and 2014. More seating areas are planned throughout the garden.

The garden space is now being used to fulfill its educational mission—to be a healing space that educates the public about the value of healing plants from many parts of the world.

In 2014, a series of videos was created featuring noted herbalists discussing particular medicinal plants in the garden. In the spring of 2015 a guided walking tour was installed—the 5 Flavors Tour. It focuses on the ways in which the taste of a plant indicates the actions it will have on the body. In November of 2015 the arboretum expanded once again, with the planting of a circle of native oaks in the area northeast of the established garden.

Over the years, Trees for Health has received funding from Urban Forestry, the James Hervey Johnson Foundation, the Steven R. Dows Memorial Fund, the Lawrence Y. True Memorial Fund at The San Diego Foundation, and private donors. Individuals can donate to Trees For Health through the Friends of Balboa Park.