Background Despite worldwide efforts to eradicate malaria over the past century, the disease remains a significant challenge in the Democratic Republic of the Congo (DRC) today. Climate change is even anticipated to worsen the situation in areas with higher altitudes and vulnerable populations. This study in Haut-Katanga, a highland region, aims to evaluate the effectiveness of past control measures and to explore the impact of climate change on the region’s distinct seasonal malaria pattern throughout the last century. Methods We integrated colonial medical records (1917–1983) from two major mining companies (Union Minière du Haut-Katanga and the Générale des Carrières et des Mines) with contemporary data (2003–2020) from Lubumbashi. Concurrently, we combined colonial climate records (1912–1946) with recent data from satellite images and weather stations (1940–2023). We used Generalised Additive Models to link the two data sources and to test for changing seasonal patterns in transmission. Results Malaria transmission in Haut-Katanga has fluctuated significantly over the past century, influenced by evolving control strategies, political conditions and a changing climate. A notable decrease in cases followed the introduction of dichlorodiphenyltrichloroethane (DDT), while a surge occurred after the civil wars ended at the beginning of the new millennium. Recently, the malaria season began 1–2 months earlier than historically observed, likely due to a 2–5°C increase in mean minimum temperatures, which facilitates the sporogonic cycle of the parasite. Conclusion Despite contemporary control efforts, malaria incidence in Haut-Katanga is similar to levels observed in the 1930s, possibly influenced by climate change creating optimal conditions for malaria transmission. Our historical data shows that the lowest malaria incidence occurred during periods of intensive DDT use and indoor residual spraying. Consequently, we recommend the systematic reduction of vector populations as a key component of malaria control strategies in highland regions of sub-Saharan Africa.