Foot-and-mouth disease (FMD) is extremely contagious and multispecies that has a severe impact on animal trade across the borders. FMD virus may cause epidemics resulting in devastation of livestock industry so, it’s worthy to explore the genomic architecture of virus to harness the mortality and morbidity particularly in cattle from Pakistan. Epithelial scrapping samples of sick animals were taken from Punjab, Pakistan and cDNA of virus was sequenced through short-read NGS Illumina technology followed by variant calling analysis to reveal how novel variants give rise to new lineage in the region for a comprehensive insight of its genomic landscape. Haplotype-based variant discovery was performed by Genome Analysis Toolkit (GATK4) with Mutect2 using Pan Asia-II as reference genome. A total of 708 variants including 642 SNPs, 38 MNPs and 28 INDELs were observed. Furthermore, whole genome annotation revealed high, low, moderate and modifier impact variants count as 10(1.28%), 514(66.15%), 115(14.80%) and 138(17.76%) respectively which are distributed in VP3, 2C, 3B and 3D proteins of FMDV. Similarly, transitions-to-transversions ratio (3.75) and missense-to-silent ratio (0.1634) across the whole genome with 639 exonic, 3 downstream, 69 intergenic and 66 upstream effects were also identified. Whereas, high impact-frame shift mutations were concentrated in 5000-7000 nucleotide positions of the genome. A worth-mentioning deletion mutation of 75bp at 5276 position harbor 2C protein. The current whole genome variant discovery of FMDV will add new insight to understand the micro-evolution, speedy emergence of strains, mutation associated disease-severity and it’s lineage to prevent the prevalence of this catastrophe.