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Sickle cell disease (SCD) and thalassemia are genetic disorders that necessitate accurate diagnosis for effective management and improved patient outcomes. The advent of nanotechnology has paved the way for innovative, precise detection methods, offering enhanced sensitivity and specificity. The present systematic review aims to assess the analytical performance of nanotechnology-based detection methods for SCD and thalassemia, with a focus on evaluating the analytical performance and identifying the most sensitive nanotechnology-based techniques. An extensive literature search was conducted across five databases (ScienceDirect, PubMed, Embase, Google Scholar), yielding 23 studies that met the inclusion criteria. These studies showcased the potential of nanotechnology-based methods for detecting SCD and thalassemia. The studies utilized diverse samples, including blood, serum, genomic DNA, and purchased oligonucleotides, with most reporting limit of detection (LOD) values. Specifically, gold nanoparticles (AuNPs) exhibited exceptional sensitivity, with detection limits ranging from 2.6 aM to 0.035 pM. Surface modification and functionalization of AuNPs significantly enhance their detection capabilities. Other nanostructures, including silver nanoparticles, quantum dots, and graphene quantum dots, also demonstrate promising diagnostic capabilities. The results showed that nanotechnology-based methods demonstrated improved analytical sensitivity, with LOD ranging from 2.6 aM to 50 nM. This systematic review provides a comprehensive overview of the analytical performance of nanotechnology-based detection methods, shedding light on their potential to revolutionize diagnosis and treatment. Overall, it highlights the transformative potential of nanotechnology in improving molecular diagnostic accuracy for SCD and thalassemia.