We have established a predictive modelling framework to systematically analyze IgG antibody responses against a large panel of P. falciparum-specific antigens and identify a predictive signature of naturally acquired immunity to malaria. Our results show that an individual's immune status can be accurately predicted by measuring IgG antibody responses to a parsimonious set of 15 target antigens. The identified immune signature is highly versatile and capable of providing precise and accurate estimates of clinical protection from malaria in demographically distinct populations. Display omitted Highlights •A predictive modelling framework has been established to analyze IgG antibody responses against a large panel of P. falciparum-specific antigens to identify a specific antigen signature of NAI.•An individual's immune status can be accurately predicted by measuring IgG responses against a small set of 15 defined parasite antigens.•Proteins identified in the 15-antigen signature represent potential candidates for next-generation malaria vaccines or biomarkers for monitoring the impact of malaria interventions.•The developed predictive framework can be adapted for developing novel surveillance and intervention tools for other infectious diseases. A large body of evidence supports the role of antibodies directed against the Plasmodium spp. parasite in the development of naturally acquired immunity to malaria, however an antigen signature capable of predicting protective immunity against Plasmodium remains to be identified. Key challenges for the identification of a predictive immune signature include the high dimensionality of data produced by high-throughput technologies and the limitation of standard statistical tests in accounting for synergetic interactions between immune responses to multiple targets. In this study, using samples collected from young children in Ghana at multiple time points during a longitudinal study, we adapted a predictive modeling framework which combines feature selection and machine learning techniques to identify an antigen signature of clinical immunity to malaria. Our results show that an individual's immune status can be accurately predicted by measuring antibody responses to a small defined set of 15 target antigens. We further demonstrate that the identified immune signature is highly versatile and capable of providing precise and accurate estimates of clinical protection from malaria in an independent geographic community. Our findings pave the way for the development of a robust point-of-care test to identify individuals at high risk of disease and which could be applied to monitor the impact of vaccinations and other interventions. This approach could be also translated to biomarker discovery for other infectious diseases.