Multidrug-resistant (MDR) microorganisms that cause septicemia are responsible for high morbidity and mortality rates among patients in extreme age groups and pose serious treatment challenges despite multipronged measures. This hospital-based study was conducted in the Postgraduate Department of Microbiology at a Tertiary Care Hospital of Kashmir (India) to investigate the prevalence and antimicrobial resistance patterns of bacteria that cause neonatal sepsis. As the resistance pattern of causative agents varies among hospitals, the study results suggest an appropriate empirical therapy for neonatal sepsis needs to be devised in our hospital. Neonatal sepsis, diagnosed by clinicians in the neonatal intensive care unit on the basis of clinical and laboratory findings, was categorized as early-onset sepsis (EOS) or late-onset sepsis (LOS) according to whether clinical presentation occurred at <72 h after birth or between 72 h and 28 days of life, respectively. Blood samples collected from 1200 neonates were cultured in a BacT/ALERT^® 3D system (bioMerieux, Inc., Durham, NC, USA). Bacterial identification and antimicrobial susceptibility tests were performed using a VITEK 2 Compact system (bioMerieux). Of the 1200 blood cultures, 126 (10.5%) were bacteremia positive. Of these 126 cultures, 73 (58%) contained gram-positive bacteria, which occurred predominantly in the EOS group (p < 0.001), whereas 53 (42%) contained gram-negative bacteria, which were equally distributed in both groups. Bacteremia was more common in the EOS group (n = 88; 70%), with Staphylococcus aureus (n = 25; 20%) being the predominant isolate, followed by Klebsiella pneumoniae (n = 20; 15.9%). In total, 38 (30%) isolates were recovered in the LOS group, with Klebsiella pneumoniae (n = 11; 9%) being predominant, followed by Acinetobacter baumannii (n = 9; 7%). Fifty-six (44.4%) and 28 (22.2%) isolates from the EOS and LOS groups, respectively, were MDR, with Staphylococcus spp. (n = 49; 38.9%), Klebsiella pneumoniae (n = 17; 13.5%), and Acinetobacter baumannii (n = 14; 11.1%) in particular showing high resistance rates. With the high prevalence of MDR infections, colistin and vancomycin can be used as initial empirical therapies in our hospital setting. This study underscores the urgent need for robust antimicrobial stewardship and infection control measures to combat the increasing threat of MDR bacterial infections in neonates.