Lassa virus is a member of the Arenaviridae family, a major cause of viral hemorrhagic fever. This virus is associated with severe neurological complications in a select group of patients. The evolutionary mechanisms behind genetic diversity, its adaptation, and its potential neuropathogenicity are still poorly understood. In this study, a comprehensive evolutionary analysis of the S and L genomes of Lassavirus was conducted, with an emphasis on ancestral reconstruction and genomic structure, as well as the identification of mutations that may contribute to viral adaptation leading to neurological disease. A set of complete S and L genomes was collected from NCBI. These sequences were carefully aligned using the MUSCLE algorithm to ensure a high match at each site. GTR+Gamma was used for evolutionary inference and was selected based on a statistical model test for its ability to accurately reflect the evolutionary dynamics of Lassa virus genomes. Phylogenetic trees were constructed using the maximum-likelihood algorithm RAxML, followed by careful preliminary analyses to assess the reliability of each branch in the tree. The mutations and recombination at the ancestral node were identified, which is likely a crucial point in the virus's ability to adapt and evolve. The emergence and distribution of major mutations across the viral lineage can be monitored. Notably, strains linked to known neurological problems frequently exhibit mutations, suggesting a possible link between certain genetic alterations and LASV's neuroinvasive characteristics. Our outcomes shed light on how genetic variety in the S and L segments impacts neurotropic virulence and offer important new insights into the evolutionary history and genomic adaptability of LASV. In order to anticipate neurological risk, create centered diagnostics, and direct the establishment of medical methods against neurotropic arenavirus infection, this study sets up the basis for future research.