Abstract Background There is a lack of information regarding the epidemiology of malaria among travellers from non-malaria endemic countries to Sahelian areas. The literature provides general statistics about imported malaria in industrialized countries or extensive recommendations about fever management, but none of these recommendations are applicable to developing countries. Methods The aim of the study was to evaluate the aetiologies of fever, malaria prevalence, and best diagnostic methods in a population of 306 non-malaria endemic travellers who, over a one-year period, consulted the French embassy’s Centre Médico-Social in Ouagadougou (Burkina Faso) for fever. All patients underwent a clinical examination, a questionnaire, and three different malaria tests: thick blood film, QBC-test and HRP-2-based rapid diagnostic test. Results Fever was caused by malaria in 69 cases (23%), while 37 (12%) were due to Pneumonia and 35 cases (8%) to ENT infections. Fever remained unexplained in 87 patients (51.3%). Malaria prevalence varied throughout the year: about 90% of malaria cases were diagnosed during and after the rainy season, between July and December, with up to 50% malaria prevalence for fever cases in October. Malaria diagnosis based solely on clinical signs, combined or not, leads to about 80% of unnecessary treatments.Although anti-malarial chemoprophylaxis was used in only 69% of short-stay patients (who travelled for less than three months), this was effective. Under local conditions, and using blood film examination as the reference method, the QBC test appeared to be more reliable than the HRP-2-based rapid diagnostic test, with respective sensitivities of 98.6% versus 84.1%, and specificities of 99.6% versus 98.3%. Conclusions Reliable biological diagnosis of malaria among travellers from non-malaria endemic countries in Sahelian areas is necessary because of low malaria prevalence and the poor performance of clinical diagnosis. A fever during the first half of the year requires investigating another aetiology, particularly a respiratory one. Malaria chemoprophylaxis is efficient and must not be overlooked. The QBC test appears to be the most reliable diagnostic test in this context.