Background: Females working in health service organizations have ever-increasing pressure to develop their career in higher positions worldwide. Therefore, the study aimed to assess factors influencing the career progression of female employees in health service organizations. Methodology: A cross-sectional mixed-method study in which a total 110 female employees from health service organizations were interviewed for quantitative survey and 15 for in-depth interviews. Results: Individual factors: career preferences, individuals’ investment on education, and individuals’ skill and hard work played a significant role in advancing career. Female employees were found to have dual responsibilities both at home and at the workplace. Their career goals were changed after marriage and having children. They face discrimination and sexual harassment and lack mentoring, coaching, and social support in the workplace. Interplay between the socio-cultural and organizational factors was evident for career growth. Maintaining the balance between work and family life with being subjected to gender stereotypes making the respondents difficult to progress in their career. Conclusion: Female employees are juggled between societal norms, family obligations, and expectations of the organization. It was recommended that each healthcare organization in Nepal needs to have a gender-balanced work environment and provide equal opportunities to women employees.