The World Health Organization (WHO) has recommended routine investigation of deletions of the histidine-rich protein 2 and 3 (HRP2/3) gene in Plasmodium falciparum (Pf). This is mainly recommended in areas endemic to Pf infection, and HRP2-based rapid diagnostic tests are utilized for malaria diagnosis. The objective of this review is to identify methodological approaches and HRP2/3 gene deletion studies that have been published in Nigeria between 2010 and 2024. MEDLINE, PUBMED, and Google Scholar databases were used systematically to find abstracts and titles, using keywords like Histidine-Rich Protein 2 gene, HRP2 gene deletion, and HRP2/3 gene deletion in Nigeria. The process for confirming and reporting HRP 2 and 3 gene deletions outlined by the WHO was followed in compiling and evaluating accepted publications. A total of 18 items were found, with eight articles meeting the criteria. Some investigations were conducted on individuals who traveled from Nigeria; others were conducted in Abuja and seven other states. It was determined that the prevalence of HRP2/3 gene deletion ranged from 78% to 0%. Study designs varied from cross-sectional data as recommended to other designs like cohort, prospective, and retrospective studies. RDT was used in studies to diagnose malaria, while microscopy was used in 87.5% of investigations to confirm the diagnosis of malaria infection. Various Pf single-copy genes were amplified using molecular techniques, including MSP1 and 2, Glurp, Pf Cox3, and β-tubulin. The review found differences in methodological approaches and insufficient data to represent the nation in each study adequately; further investigation in other states is recommended.