Coral aquaculture is an emerging aquaculture industry. In recent years, ciliate infestation has become a serious hazard to wild and captive corals. Our previous research found that infected corals can fester or die within 72 h, posing a serious threat to large-scale coral aquaculture. Little research has been done on the treatment of coral ciliate disease. Therefore, drugs that seek effective treatment and avoid stress responses to corals will be applied to large-scale coral aquaculture. Forsythia suspensa is a common traditional Chinese medicine with anti-inflammatory, anticancer, antibacterial, antiviral, and insecticidal functions. In this study, the F. suspensa extract at concentrations of 0.5%, 1%, 1.25%, 1.75%, 2.25%, and 2.75% was used to conduct a virulence test on ciliates and evaluate the therapeutic effect on Goniopora columna. The uninfected ciliates are the N-group, and the infected ciliates without drug treatment, the control group, are the C-group. After the experiment, the effects of the F. suspensa extract on the ciliate stress response of corals were evaluated by using the virulence test and calculating damage to histopathology, zooxanthellae, chlorophyll a, and three antioxidant enzymes, namely, superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA). The results showed that the LC50 value of the F. suspensa extract was approximately 1.52%, and when the concentration was increased to 1.75%, the ciliates could be completely killed within 10 min of medicated bathing. The SOD, CAT, and MDA of G. columna under the 1.75% treatment were lower than those of the other treatment groups and higher than only those of the N-group. The zooxanthellae, chlorophyll a, and survival rate were not significantly different from those in the N-group. Upon histological examination, no ciliates or vacuum were found in coral tissue 72 h after treatment. In conclusion, 1.75% Forsythia suspensa extract is effective in the treatment of G. columna ciliate infection without causing a strong stress response in corals. Forsythia suspensa can be effectively applied in the prevention of ciliate diseases in large-scale coral aquaculture.