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Background Neonatal sepsis includes numerous systemic illnesses such as septicemia, meningitis, urinary tract infections, and pneumonia. In developing countries, the major reason for neonatal mortality is septicemia, which accounts for almost 50% of overall deaths. Thrombocytopenia is one of the most common hematological problems during the neonatal period, affecting the majority of sufferers admitted to the neonatal intensive care unit (NICU). The aim of our study was to find the frequency of thrombocytopenia and its severity in neonates with sepsis. Methods The study was conducted at the Department of Hematology at Khyber Medical University, Peshawar, Pakistan. A total of 170 neonates with an age of fewer than 28 days, both genders, and positive blood cultures were included in the study using a non-probability consecutive sampling technique. Data was recorded in predesigned questionnaires after taking informed consent. Data were recorded and analyzed using SPSS version 26 (IBM Corporation, Armonk, NY, USA). Results Of the 170 neonates, 104 (61.2%) were males, with a mean age of 12.12±8.88 days. The majority of the babies 73 (42.9%) were in the age group of 0-7 days. Most of the neonates 72 (42.4%) were born via normal vaginal delivery (NVD). Of the neonates, 117 (68.82%) presented with fever, and 105 (61.76%) were reluctant to feed. Furthermore, 65.29% of the neonates had thrombocytopenia, of which 34 (20%) had mild, 43 (25.3%) had moderate, and 34 (20%) had severe thrombocytopenia. In neonates with positive blood culture, the platelet level was low (p0.001). In the case of gram-negative organisms, the level of platelets was lower as compared to gram-positive organisms (p0.001). Conclusion Sepsis is still a common cause of newborn thrombocytopenia. The fact that it is present in more than half of all culture-positive sepsis episodes indicates the severity of the condition. This condition is further defined by higher percentages of early-onset gram-negative septicemia compared to gram-positive sepsis.