Blood transfusions represent a small but significant source of malaria transmission. Most blood banks rely solely on donor questioning to exclude malaria patients from donating blood. No guidelines exist for in vitro screening of donor blood for malaria in endemic areas. Possible laboratory screening techniques include: microscopy; enzyme-linked immunosorbent assay (ELISA) antibody testing; polymerase chain reaction (PCR) testing; and rapid diagnostic antigen tests. However, all these modalities have diagnostic limitations. Based on a best evidence review, we present recommendations using an algorithmic approach to blood screening for malaria in Pakistan. This algorithm considers regional endemicity for malaria, as well as a detailed donor history, in order to decide whether donor blood should be tested with rapid antigen testing. We hope this algorithm will assist in the development of future national guidelines for screening blood for malaria that will reduce the risk of blood-borne transmission.