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Introduction Bhutan is progressing toward malaria elimination. The purpose of this evaluation was to assess the ability of the surveillance system from 2006 to 2012 to meet the objectives of the Bhutan Vector-borne Disease Control Program (VDCP) and to highlight priorities requiring attention as the nation transitions to elimination. Methods The evaluation was conducted using the Center for Disease Control guidelines for evaluating public health surveillance systems. Data sources included a search of publically available literature, VDCP program data, and interviews with malaria surveillance personnel. Blood slide quality assurance and control through formal assessment of slide preparation and measures of between-reader correlation were performed. Results Total malaria cases declined from 2006 to 2012. The average slide positivity rate decreased from 3.4% in 2006 to 0.2% in 2012. The proportion of non-residents in all cases increased to its highest value of 22.6% in 2012, and significant clustering in the border regions of India was noted, with Sarpang accounting for more cases than any other district from 2009 onward. Case detection was almost exclusively passive, but flexibility and sensitivity was demonstrated by the later addition of active case detection and specification of imported and locally acquired cases. Spatial data were limited to the village level, not allowing identification of transmission hotspots. For blood smears, statistical measures of between-reader agreement and predictive value were not computed. Blood smear quality was suboptimal by at least one criterion in over half of evaluated smears. Timeliness in reporting of cases was on a weekly to monthly basis, and did not meet the WHO goal of immediate notification. Conclusion As of 2012, the national malaria surveillance system demonstrated flexibility, representativeness, simplicity, and stability. The full potential for data analysis was not yet realized. Attaining the goal of malaria elimination will require system function enhancement through increased and more accurate case detection and rapid investigation, improved health worker training and accountability, focally targeted response measures, and, in particular, the challenge of finding re-introductions of infections from India. Many such measure have been undertaken or planned as part of the next phase of the Bhutan’s National Strategic Plan.