Falsified drugs are of serious concern to public health worldwide, particularly for developing countries where quality control of drugs is inefficient. In law enforcement against such fake medicines, there is a need to develop reliable, fast, and inexpensive screening methods. In this work, the ability of an innovative low-cost handheld near-infrared spectrometer to identify falsifications among two antimalarial fixed dose combination tablets, dihydroartemisinin/piperaquine and sulfadoxine/pyrimethamine, has been investigated. Analyzed samples were collected in Burkina Faso mainly in rural transborder areas that could be infiltrated by illicit drugs. A principal component analysis was applied on the acquired near-infrared spectra to identify trends, similarities, and differences between collected samples. This allowed to detect some samples of dihydroartemisinin/piperaquine and sulfadoxine/pyrimethamine which seemed to be falsified. These suspicious samples were semiquantitatively analyzed by thin-layer chromatography using Minalab® kits. Obtained results allowed to confirm the falsifications since the suspected samples did not contain any of the expected active pharmaceutical ingredients. The capacity of the low-cost near-infrared device to identify specifically a brand name of dihydroartemisinin/piperaquine or sulfadoxine/pyrimethamine has been also studied using soft independent modelling of class analogy (SIMCA) in the classical and data driven versions. The built models allowed a clear brand identification with 100% of both sensitivity and specificity in the studied cases. All these results demonstrate the potential of these low-cost near-infrared spectrometers to be used as first line screening tools, particularly in resource limited laboratories, for the detection of falsified antimalarial drugs.