Summary Background Palatal dysfunction is a common cause of poor performance in racehorses. Although conservative management resolves just over 60% of cases, there is a requirement for further intervention in the residual 40% of cases that do not respond. It is proposed that a palatal stiffening technique that is simple to perform, safe, minimally invasive and enables a rapid return to exercise would be an acceptable first intervention. Genipin is a self‐polymerising molecule that bonds to collagen matrices increasing tissue strength, stiffness and resilience. A previous study demonstrated that implanted genipin increased palatal strength and its resistance to deformation and potentially was effective in decreasing likelihood of palatal dysfunction in horses. Objectives The objective of the study was to appraise the safety and feasibility of implanting genipin oligomers into the equine soft palate and to report on racehorse trainers' subjective assessment of its usefulness in management of palatal dysfunction. Study design Prospective, non‐randomised, pilot study. Methods Fifty Thoroughbred racehorses diagnosed with palatal dysfunction were implanted transendoscopically with genipin. The horses were monitored for adverse reactions during hospitalisation. A standard questionnaire provided to the horses' trainers was used to record additional adverse reactions and satisfaction with the animals' subsequent performance. Post‐treatment dynamic endoscopy was performed in a subgroup of animals. Results One horse developed adverse clinical signs of pyrexia and reduced appetite, which responded to treatment. Post‐procedural endoscopic examination revealed mild palatal abnormalities in 6 of 50 horses that showed no clinical signs. One horse had mild generalised oedema, four with mild focal swelling and one with a superficial mucosal ulceration at a single site of implantation of the soft palate. Following treatment, 76% of horses were reported to show clinical improvement by their trainers with 24% reported not to show improvement. Main limitations The study was not controlled, and outcome measures were mainly subjective. Conclusions The procedure was well tolerated, safe, minimally invasive and enabled a rapid return to exercise. Trainer reported improvement was comparable to previously reported palatoplasty procedures.