Abstract Background Invasive non-typhoidal Salmonella (iNTS) disease is a major public health threat in developing countries, yet molecular epidemiological data from Ghana remain limited. This study characterizes the phylogenomic profiles and antimicrobial resistance determinants of iNTS isolates recovered from human blood cultures in Ghana. Methods Over an eight-year surveillance period (2016–2023), thirty-one (31) iNTS blood culture isolates—drawn from a total of 271 bacterial pathogens identified—underwent whole-genome sequencing on the Illumina NovaSeq platform. The iNTS isolates’ genomic data were analyzed for serovar distribution, MLST profiles, Antimicrobial resistant (AMR) genes and virulence markers including plasmids and Salmonella Pathogenicity Islands (SPIs). Clades of Salmonella enterica serovar Typhimurium ST 313 and lineages of Salmonella enterica serovar Enteritidis ST11 were determined referencing regionally important circulating strains. Results S . Typhimurium and S . Enteritidis together constituted 67.7% (21/31) of iNTS isolates circulating in Ghana, whereas the remaining serovars were largely confined to isolates obtained within the past three years of the study period. S . Typhimurium ST 313 strains were of the L2 and L3 lineages which are associated with invasive disease in sub-Sahara Africa while S. Enteritidis ST 11 isolates clustered with the Global Epidemic and Central East Africa clades which are linked to widespread transmission and sub-Sahara African regional adaptation. All iNTS isolates harboured several SPIs known for invasiveness while 77.4.0% (24/31) carried plasmids including IncFIB(S) and IncFII(S). Nearly half (48.8%, 15/31) of the isolates carried at least one AMR gene with about 30.0% (9/31) harboring multiple AMR genes conferring resistance to three or more antibiotic classes. The commonest AMR gene identified was the blaTEM-1 gene coding for beta lactamase enzyme while quinolone resistant gene (qnrS1) was the least common. Conclusion Circulating iNTS pathogens in Ghana are diversified including S . Typhimurium ST313 lineages and S . Enteritidis ST 11 clades regionally known for invasive disease. These strains carry remarkable markers of virulence highlighting the need for enhanced surveillance and institution of preventive policies. Our findings highlight the utility of whole-genome sequencing for tracking circulating iNTS lineages and strengthening public health surveillance in Ghana.