In stable transmission areas, malaria is the leading cause of anemia in children. Anemia in children is proposed as an added sensitive indicator for community changes in malaria prevalence. We report short-term temporal variations of malaria and anemia prevalence in rural Malawian children. Data from five repeated cross-sectional surveys conducted over 1 year in rural communities in Chikwawa District, Malawi, were analyzed. Different households were sampled per survey; all children, 6–59 months, in sampled household were tested for malaria parasitemia and hemoglobin levels using malaria rapid diagnostic tests (mRDT) and Hemocue 301, respectively. Malaria symptoms, recent treatment (2 weeks) for malaria, anthropometric measurements, and sociodemographic details were recorded. In total, 894 children were included from 1,377 households. The prevalences of mRDT positive and anemia (Hb < 11 g/dL) were 33.8% and 58.7%, respectively. Temporal trends in anemia and parasite prevalence varied differently. Overall, unadjusted and adjusted relative risks of anemia in mRDT-positive children were 1.31 (95% CI: 1.09–1.57) and 1.36 (1.13–1.63), respectively. Changes in anemia prevalence differed with short-term changes in malaria prevalence, although malaria is an important factor in anemia.