The current study investigates the incidence of subclinical mastitis (SCM), associated risk factors, involvement and antimicrobial susceptibility of Staphylococcus aureus in the development of SCM in District Faisalabad of Pakistan. For this purpose, a total of 384 goat milk samples were screened for SCM through surf field mastitis test (SFMT) and mastitis-positives cases were further investigated for isolation of S. aureus using standard procedures. Coagulase gene was PCR amplified from the clinical isolates to categorize them into Coagulase positive Staphylococci (CPS) and coagulase negative Staphylococci (CNS). A questionnaire was used to record risk factors associated with occurrence of SCM and results were analyzed using non-probability statistical analysis. Results indicated that an overall 63.28% (243/384) of goats were found positive for SCM, of which 58.85% (143/243) revealed Staphylococcal growth among them 69.93% (100/143) were CPS, while 30.07% (43/143) were found as CNS. Drug susceptibility against penicillins, cephalosporins, macrolides and other drugs showed that 50% of CPS and 30% of CNS were found multi-drug resistant-exhibiting resistance against more than two or more than two classes of drugs. None of the CPS while 20 % from CNS isolates were 100% susceptible to all kinds of drugs tested. Finally, age, grazing system, use of beta-lactam antibiotics, parity, and poor hygiene were potential risk factors. Altogether, the study concluded high incidence of SCM and isolation rate of staphylococci that were found resistant against most of the commonly used antibiotics.