This is the first randomised controlled clinical trial comparing natamycin 5% eye drops alone to natamycin 5% and chlorhexidine 0.2% combination eye drops for the treatment of fungal keratitis, an infection to the front of the eye that can lead to blindness if not treated appropriately. In this article we describe how we plan to conduct this clinical trial. The primary analysis will be a comparison by arm of best spectacle corrected visual acuity at 3 months, i.e. how well patients can see with glasses if needed at the end of the study period.