The U.S. President's Malaria Initiative-funded MalariaCare project implemented an external quality assurance scheme to support malaria diagnostics and case management across a spectrum of health facilities in participating African countries. A component of this program was a 5-day, malaria diagnostic competency assessment (MDCA) course for health facility laboratory staff conducting malaria microscopy. The MDCA course provided a method to quantify participant skill levels in microscopic examination of malaria across three major diagnosis areas: parasite detection, species identification, and parasite quantification. A total of 817 central-, regional-, and peripheral-level microscopists from 45 MDCA courses across nine African countries were included in the analysis. Differences in mean scores with respect to daily marginal performance were positive and statistically significant (P < 0.001) for each challenge type across all participants combined. From pretest to assessment day 4, mean scores for parasite detection, species identification, and parasite quantification increased by 19.1, 34.9, and 38.2 percentage points, respectively. In addition, sensitivity and specificity increased by 20.8 and 13.8 percentage points, respectively, by assessment day 4. Furthermore, the ability of MDCA participants to accurately report Plasmodium falciparum species when present increased from 44.5% at pretest to 67.1% by assessment day 4. The MDCA course rapidly improved the microscopy performance of participants over a short period of time. Because of its rigor, the MDCA course could serve as a mechanism for measuring laboratory staff performance against country-specific minimum competency standards and could easily be adapted to serve as a national certification course.