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, however, 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 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 glycoprotein gene yielded a 420 bp product and the phylogenetic tree revealed that the Pakistani BEF virus isolates clustered closely with strains from Iran, India and Australia indicating a strong genetic resemblance. The overall prevalence was 13.83% (65/470) which significantly higher in cattle (15.49%) than in buffaloes (3.70%), and cattle had significantly higher chance of infection than buffaloes (odds ratio = 4.31, confidence interval = 1.33 - 13.95). This study provided the first comprehensive gene sequencing data on BEF in Pakistan, significantly enhancing the global understanding of the virus through detailed molecular and phylogenetic analysis.