(1) Background: Angola is among the high-burden countries with malaria cases globally. After 2013, we suspected an increase in the number of malaria cases in Cubal (Angola), previously in decline. Our objective was to evaluate the incidence rate in Cubal, overall and by neighborhood, for 2014, 2015, and 2016. (2) Methods: A retrospective, observational study was performed in Cubal (Angola) from January 2014 to December 2016, including all patients with a microbiologically confirmed diagnosis, treated at Cubal’s Hospitals for this period of time. The principal variables calculated were the incidence rates of 2014, 2015, and 2016 in Cubal (overall and by neighborhood). (3) Results: There were 3249 malaria cases. The incidence rates were 2.27, 10.73, and 12.40 cases per 1000 inhabitants in 2014, 2015, and 2016, respectively. In the neighborhood, Hamavoko-Kasseke, there was a 10.73-fold increase in incidence during this period. Additionally, Hamavoko-Kasseke presents an anomalous distribution of malaria cases. (4) Conclusions: We observed an increase in the incidence of malaria in Cubal during the three-year study period. The case distribution was highly heterogeneous with hyperendemic areas, and we found a chronobiological association between the construction of a civil engineering project. This information could be useful for deciding which malaria control strategies must be implemented in this area.