Equine trypanosomosis comprises different parasitic diseases caused by protozoa of the subgenus Trypanozoon : Trypanosoma equiperdum (causative agent of dourine), Trypanosoma brucei (nagana) and Trypanosoma evansi (surra). Due to the absence of a vaccine and the lack of efficacy of the few available drugs, these diseases represent a major health and economic problem for international equine trade. Development of affordable, sensitive and specific diagnostic tests is therefore crucial to ensure the control of these diseases. Recently, it has been shown that a small RNA derived from the 7SL gene (7SL‐sRNA) is produced in high concentrations in sera of cattle infected with Trypanosoma congolense , Trypanosoma vivax and Trypanosoma brucei . Our objective was to determine whether 7SL‐sRNA could serve as a marker of active infection in equids experimentally infected with Trypanosoma equiperdum by analyzing the sensitivity, specificity and stability of the 7SL‐sRNA. Using a two‐step RT‐qPCR, we were able to detect the presence of 7SL‐sRNA between 2 and 7 days post‐infection, whereas seroconversion was detected by complement fixation test between 5 and 14 days post‐infection. There was a rapid loss of 7SL‐sRNA signal from the blood of infected animals one day post‐trypanocide treatment. The 7SL‐sRNA RT‐qPCR allowed an early detection of a treatment failure revealed by glucocorticoid‐induced immunosuppression. In addition, the 7SL‐sRNA remains detectable in positive sera after 7 days of storage at either 4 °C, room temperature or 30 °C, suggesting that there is no need to refrigerate serum samples before analysis. Our findings demonstrate continual detection of 7SL‐sRNA over an extended period of experimental infection, with signals detected more than six weeks after inoculation. The detection of a strong and consistent 7SL‐sRNA signal even during sub‐patent parasitemia and the early detection of treatment failure highlight the very promising nature of this new diagnostic method.