In areas where malaria is endemic and microscopes are unavailable, rapid diagnostic tests (RDTs) are essential tools for early diagnosis and prompt and effective treatment. However, HRP2-based RDTs are threatened by the emergence of Plasmodium falciparum parasites that do not carry the pfhrp2 or pfhrp3 gene, leading to false-negative results. Therefore, the aim of this study was to evaluate the performance of the ParaHIT RDT together with the proportion of pfhrp2/3 gene–deleted P. falciparum parasites in Togo. The performance of RDTs compared with microscopy and polymerase chain reaction (PCR) was determined using capillary blood collected by finger prick during a cross-sectional study conducted from September 2021 to January 2022 in children aged 6–59 months at two sentinel sites. Blood spots were collected for molecular analysis. Amplicons from the target regions (exon 2 of hrp2 and hrp3 genes) were generated by multiplex nested PCR and sequenced using Illumina’s MiSeq protocol. A total of 278 samples were analyzed for ParaHIT RDT evaluation. The sensitivity and specificity of the RDT test compared with microscopy were 96.4% and 85.7%, respectively, which increased to 97.9% and 90.7%, respectively, when compared with PCR. Of the microscopically and PCR-positive P. falciparum samples, 138 were sequenced to detect pfhrp2/3 deletions. None of the parasites had a single pfhrp2 deletion or a single pfhrp3 deletion. The ParaHIT RDT demonstrated an acceptable level of performance in this evaluation, confirming the use of HRP2-based RDTs for the detection of P. falciparum infection in areas where microscopy is not available in Togo.