Molecular diagnostics have revolutionized viral disease diagnosis in clinical settings, offering rapidity, sensitivity, and specificity. Nigeria’s diverse burden of viral diseases, coupled with resource limitations and underreporting, underscores the critical need for efficient molecular diagnostics. The article traces the progressive trajectory of molecular diagnostics in Nigeria, including the establishment of Lassa virus detection, containment of the Ebola virus outbreak, and the pivotal role of the Nigeria Center for Disease Control (NCDC). It also highlights the impact of the COVID-19 pandemic on expanding molecular diagnostics infrastructure. Despite these advancements, challenges such as limited testing capacity, skilled personnel shortages, and inadequate funding persist. The article recommends measures to address these challenges, emphasizing the transformative potential of molecular diagnostics in viral surveillance and management. Overall, it underscores the importance of strategic planning and concerted efforts to enhance the utilization of molecular diagnostics in Nigeria’s healthcare system.