Rapid and accurate strain identification of Neisseria meningitidis is essential during outbreaks. N. meningitidis poses a serious threat due to its potential to cause rapid onset meningitis and sepsis, both presenting with high mortality rates. This study aimed to validate Oxford Nanopore Technologies long-read sequencing as a rapid alternative to Illumina short-read sequencing for strain characterization of N. meningitidis and early outbreak detection. 51 isolates were DNA-extracted using both QIAsymphony SP and MagLEAD 12gc. Samples extracted with QIAsymphony were sequenced on the Illumina platform, while those processed with MagLEAD were sequenced using the Oxford Nanopore platform, using the Rapid PCR barcoding kit for library preparation. Sequencing data were analyzed using Ridom Seqsphere+5.0.0. for de novo assembly and typing. Illumina reads were assembled with Velvet, while Nanopore reads were basecalled with Dorado, assembled using Flye, and polished with Medaka. Final assemblies from both platforms were analyzed using cgMLST within Seqsphere+ and submitted to PubMLST for genomic comparison and outbreak cluster visualization. The results from the genomic comparison showed a slightly higher mean number of allelic errors for Nanopore compared to Illumina, however, the difference was not statistically significant. The increased number of errors may be explained by PCR bias, reducing the coverage and leading to more errors in those samples. The grapetree analysis showed that both platforms produced nearly identical clustering patterns, successfully identifying outbreak-related isolates in all but one case, validating Nanopore’s capability for reliable strain-level resolution in epidemiological surveillance.