Ageratina pichinchensis is utilized in traditional medicine for the treatment of dermatomycosis and inflammation. The aim of this study was to evaluate the clinical and mycological effectiveness of the topical administration of an enecalin standardized extract of A. pichinchensis for treating onychomycosis in patients with type 2 diabetes mellitus (DM2). A double blind, randomized, and controlled clinical trial was carried out that included patients with DM2 and who had mild or moderate onychomycosis. Participants were administered topically, for 6 months, a lacquer containing the encecalin standardized extract of A. pichinchensis (experimental group) or 8% ciclopirox (control group). In a large percentage of both, the control group (77.2%) and the experimental group (78.5%), clinical efficacy was detected as a decrease in the number of affected nails and a reduction in the severity of nail involvement. Without exhibiting statistically significant differences between groups, the encecalin standardized extract of A. pichinchensis was clinically and mycologically effective in the treatment of mild and moderate onychomycosis in patients with DM2. The treatment of onychomycosis in patients with DM2 implies a greater challenge, while control of blood glucose levels in these patients, played a very important role in the response of patients to treatment.