Background: Staphylococcus epidermidis is an important cause of nosocomial infections in children. The study undertaken identified antibiotic resistance markers among biofilm-forming S. epidermidis. Methods: A total of 105 bacteremia-positive samples from hospitalized children were processed for identification of S. epidermidis using species-specific rdr gene. Phenotypic antibiotic resistance was checked through Kirby-Bauer disc diffusion method. 96-well microtiter plate assays and PCR were used for biofilm production and antibiotic-resistant genes, respectively. Results: Among 105 clinical isolates, rdr gene was detected in 34 (32.38%) isolates. The rdr detected isolates exhibited biofilm formation (n = 34; 100%). Multidrug-resistant (MDR) pattern was observed among S. epidermidis, while the frequency of MDR was higher in very strong biofilm-forming S. epidermidis (n = 18; 52.9%, p ≤ 0.002) as compared to weak biofilm-forming S. epidermidis (n = 6; 17.6%). All S. epidermidis strains were resistant to cefoxitin, penicillin, and augmentin (n = 34; 100%). High resistance was observed against erythromycin (n = 29; 85.29%) and ciprofloxacin (n = 25; 73.5%). S. epidermidis displayed complete susceptibility (n = 34; 100%) toward vancomycin, tetracycline, and linezolid. Among the S. epidermidis isolates, the methicillin resistance gene (mecA, n = 29; 85.2%, p ≤ 0.000), the erythromycin resistance gene (msrA, n = 19; 55.7%) and the beta-lactamase resistance gene (blaZ, n = 17; 50%) were detected. Detection of mecA (n = 17; 94.4%), msrA (n = 8; 44.4%) and blaZ (n = 11; 61.1%) significantly (p ≤ 0.0052) correlated with very strong biofilm-forming S. epidermidis. Conclusion: Biofilm formation is significantly associated with antibiotic resistance. The study's result will help to understand the molecular mechanism of antimicrobial resistance in biofilm-forming S. epidermidis among pediatric patients.