The key to the effective management of malaria is prompt and accurate diagnosis followed by effective treatment. The aim of this study was to determine asymptomatic malaria parasite prevalence and density and evaluate the performance characteristics of the Partec CyScope ® (fluorescent microscope) in school children in the Mount Cameroon region using light microscopy as a gold standard. A total of 541 pupils aged 4 -16 years were recruited into the study. After recording demographic data on each child, capillary blood was collected for the preparation of thin and thick blood films for the assessment of parasite density and speciation respectively. Five µl of blood was placed on the dye-labeled portion of the slide, cover-slipped, incubated for 1 minute and observed under the CyScope ® for parasites. Performance characteristics of CyScope ® were calculated. The overall prevalence of malaria was 64.0% and 58.4% for light microscopy and Partec CyScope ® respectively. The overall geometric mean parasite density (GMPD) was 2255.22 (range 320-35040). The sensitivity of the test was 91.3% while the specificity was 86.7%. The Partec CyScope ® showed a relatively high sensitivity and specificity in diagnosing malaria in school children and could therefore be used in mass surveillance programmes for the management and control of malaria.