This study examined the impact of job autonomy on employee performance in selected Federal government hospitals in Delta and Edo States, Nigeria. Job autonomy, a critical element of employee empowerment, was analyzed through four dimensions: flexible work schedules, flexible working hours, participation in decision-making, and clear work criteria. Questionnaire was employed as the research instrument for this study with 170 respondents deemed usable and the study relied on the Agency Theory as its theoretical framework. Data collected were analysed using Pearson’s coefficient of correlation and linear regression analysis with the aid of Statistical Package for Social Sciences (SPSS) Version 23. The findings affirmed that flexible work schedules enable employees to balance professional and personal responsibilities, reducing stress and enhancing job satisfaction. Similarly, flexible working hours were found to improve employee engagement and productivity by allowing individuals to align their work times with their peak performance hours. The study recommends among others that hospital administrators in Federal government hospitals in Delta and Edo States should implement policies that promote flexible work schedules. Flexibility can allow healthcare workers to balance their professional and personal lives, reducing stress and improving job satisfaction, among others.