Globally, neonates with sepsis contribute to nearly a third of the 2.3 million neontal deaths annually due to gaps associated with poor diagnosis, insufficient referral networks and caregiver delays. These gaps disproportionately affect children of rural dwellers in Ghana. This research investigated diagnostic capacity and clinical outcomes of neonates with sepsis admitted to health facilities in Gushegu and Nkwanta South districts. Both the Health Systems Framework and the Three Delays Model were used to establish and analyze all gaps and present findings. A convergent mixedmethods design was employed in target facilities 322 neonatal records were reviewed, and interviews conducted with caregivers and health workers. Data were collected between March and June 2021 after ethical approval were obtained from Ghana Health Service’s Institutional Review Board (GHS-ERC 008/03/20). Among the 322 subjects, 58% were women with 70% were receiving below GHS 500 as montly income. In Gushegu, formal education among caregivers was low (43%) with the average trips to the facilities above 2 hours. In all facilities studied, none provided for C-reactive protein (CRP) or blood culture test. In both districts, recovery rates were relatively low, Gushegu (52%) and Nkwanta South (64%), while the rates of death were lower at 20% and 14%, respectively. Late presentation (>48 hours) tripled poor outcomes (OR = 2.8), delayed intravenous antibiotics (>6 hours) increased death at almost four times (OR = 3.9) and delayed referral (12 hours or longer) doubled mortality risk considerably (OR = 2.1). Only 31% of health workers had recieved recent training. Diagnostic bottlenecks, delayed referral, and systemic weaknesses in neonatal-care institutions led to significant morbidity and mortality. Besides, the presence of sociodemographic underprivileged and bad knowledge of caregivers all contribute to the time delay towards seeking help by the patient. It is essential to bridge these gaps to promote decreased neonatal mortality in rural Ghana. Recommendations come from strengthening medical diagnostic infrastructure as well as the development of new clinical guidelines and referral systems, integrating neonatal sepsis indicators to the District Health Information Management System, version 2 (DHIMS2), and enhancing caregiver training and financial support systems.