Bovine ephemeral fever (BEF) is a re-emerging arbovirus infection, causing substantial economic losses primarily attributed to decreased milk production. BEF is a frequently reported disease in Pakistan, but there is a lack of scientific data, particularly regarding gene sequencing and phylogenetic analysis of this viral infection in bovines. This research was planned for the molecular detection of the BEF virus in dairy animals of Sindh province, Pakistan. The association of various risk factors, including seasonal variation, species, breed, sex, age, lactation, and feeding pattern, was also analyzed. A total of 470 blood samples from cattle and buffaloes were collected across different topographical regions of Sindh from 2021-2022, and subjected to molecular detection through reverse transcriptase PCR (RT-PCR). Sequencing of positive RT-PCR amplicons and phylogenetic analysis were then performed. A questionnaire was designed to get comprehensive information about each animal before sample collection to develop an association between various risk factors. RT-PCR amplification of the G gene yielded a 420 bp product, and the phylogenetic tree revealed that the Pakistani BEFV isolates clustered closely with strains from Iran, India, and Australia, indicating a strong genetic resemblance. The overall prevalence was 13.82% (65/470) which significantly higher in cattle (15.49%) than in buffaloes (3.7%), and cattle had significantly higher chance of infection than buffaloes (OR=4.31, CI=33-13.95). This study provides the first comprehensive gene sequencing data on BEF in Pakistan, significantly enhancing the global understanding of the virus through detailed molecular and phylogenetic analysis.