This protocol describes the Pathways Study, a realist evaluation investigating how informal social ties, relationships, and communication among health workers influence the quality of neonatal care in two Kenyan public hospitals. The study uses mixed methods including observation, social network analysis, interviews, and focus groups to develop a programme theory that can inform interventions targeting health worker behaviours. Findings aim to address Kenya's persistently high neonatal mortality rate by improving understanding of the 'software' aspects of the health workforce.