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Infectious diseases that cause illness and/or death in humans can be contracted from mosquito bites. A viable and alternate method of personal protection that can lower the danger of human exposure to mosquito-borne diseases is the use of plant-based repellents. Using a high-throughput screening system, the current work examined the toxicity, contact irritancy, and spatial repellency of Andrographis paniculata crude extract and its fractions against Aedes aegypti, Anopheles minimus, and An. dirus. Five fractions (i.e., F1, F2, F3, F4, and F5) were separated from the crude extract by column and thin layer chromatography and analyzed using high-performance liquid chromatography and mass spectrometry. The major active compounds identified from F3 and F5 were 4-deoxy-11,12-didehydroandrographolide and andrographolide. Three concentrations (1.0, 2.5, and 5.0%) for each of the crude extracts and the five fractions were individually impregnated on nylon netting strips and evaluated against the three mosquito species. Results showed that the highest contact irritancy was elicited by the crude extract at 5% concentration against Ae. aegypti (43.70% escaped). Results of the spatial activity index (SAI) showed that fractions F3 and F5 at 2.5% demonstrated the strongest repellency against Ae. aegypti (SAI = 0.84) and An. minimus (SAI = 0.83), respectively. Both the crude extract and its components did not cause any knockdown or mortality. These findings suggest that fractionation of A. paniculata extracts is valuable in assessing their spatial repellent efficacy against mosquitoes. Fractions F3 and F5 hold promise as natural mosquito repellents and could contribute to developing effective mosquito control strategies.