Malaria clinical data from health facility records are used for evaluating control programmes’ impact and providing insights of epidemiological situation. In the present study we assessed trend of malaria admissions between 2009 and 2012 in rural and urban health facilities of the district of Kandi, a very arid area with particularly severe drought lasting up to 6 months. Curative care records in the Gansosso urban health facility and Sonsoro rural health facility were consulted and all uncomplicated and severe cases of malaria in local population between 2009 and 2012 were reported. For each malaria case, information on age, gender, origin of the patient were collected on electronic forms using tablets installed with Open Data Kit (ODK) Collect. Characteristics of patients positive to malaria, change in age groups and monthly variation were compared between the urban and rural health facilities. Of the 21,008 febrile patients consulted, a total of 7,990 cases (38%; 95% CI 37-39) were detected positive to malaria by the means of RDTs or microscopy. The number of confirmed malaria cases in rural and urban Kandi were respectively 2,911 (36%, 95% CI 35-37) and 5,079 (39%, 95% CI 38-40) (p<0.001). Severe cases were recorded at a lower frequency in the rural health facility, as compared to the urban one (1% vs 25%, p<0.001) with most of cases diagnosed in patients from neighbouring villages. Both facilities records showed higher prevalence in females as compared to males (51% vs 49%; p =0.97). At rural Kandi, the age group hardest hit was under 5 years representing 40% (95% CI: 38-42) while in urban Kandi, malaria prevalence was higher in the age group older than 15 years (53%; 95% CI: 52-54). Between 2009 and 2012, monthly malaria prevalence was generally higher in rural areas than in urban ones. Except for 2012, peaks of malaria cases occurred earlier in the rural area than in the urban area. Our study indicated that malaria occurs throughout the year, regardless of the seasons, and affected all age groups in both rural and urban localities. This is of a programmatic interest in designing and planning vector control interventions particularly in endemic settings.