Bovine mastitis caused by Klebsiella pneumoniae poses significant economic and health challenges in dairy production, particularly in its subclinical form. In this study, milk samples (n = 305) from different cattle breeds of Red Sindhi, Sahiwal, Cholistani, and Holstein Friesian were collected from six dairy farms in Pakistan. The prevalence of subclinical mastitis ranged from 42.3% in Red Sindhi to 77.0% in Sahiwal breeds, with an overall prevalence of 56.39%. The prevalence of K. pneumoniae was 11.8% (36/305), varying significantly among breeds: Cholistani (26.2%), Red Sindhi (17.3%), Holstein Friesian (5.0%), and Sahiwal (0%). Farm-specific prevalence ranged from 0% to 26.2%, underscoring the influence of local management practices. All tested microorganisms remained sensitive to cefotaxime, meropenem, and ciprofloxacin but revealed 100% resistance to ampicillin and 80.5% and 69.4% resistance to amoxicillin and streptomycin, respectively. Molecular analysis detected the blaTEM in 91.6% of isolates. These findings highlight significant breed and farm-level differences in subclinical mastitis and resistance patterns. The predominance of blaTEM and full susceptibility to third-generation cephalosporins suggest that local K. pneumoniae isolates may differ from global trends. Strengthened farm management and prudent antimicrobial use are essential to limit infections and safeguard both animal and public health.