Background: According to the World Health Organization (WHO), the shortage of human resources in the healthcare sector has shown a growing trend year by year. Notably, there is a significant shortage, inadequate distribution, and high turnover of licensed professionals, influenced by various factors. Aim: This study aimed to examine healthcare workers’ turnover intentions and the influencing factors in referral healthcare organizations in Ulaanbaatar city. Materials and Methods: The study employed a cross-sectional study using quantitative research methods was conducted during 2024–2025. A total of 150 healthcare workers from central hospitals, maternity hospitals, and district health centers participated. The standardized questionnaire developed by Auerbach et al. (2013) was used to assess turnover intention. Data were analyzed using SPSS 26.0 software. Results: Of the participants, 38% were from central hospitals, 33.3% from maternity hospitals, and 28.6% from district health centers. The majority (85.3%) were female. In terms of profession, 44.6% were doctors, 34.6% nurses, and 20.6% comprised paramedics, public health specialists, laboratory physicians, pharmacists, and midwives. Regarding retention, 78% of participants intended to continue working in the healthcare sector until retirement, while 35.3% expressed an intention to leave in the near future. Statistically significant differences in turnover intention were observed by age and profession. Younger employees demonstrated a higher intention to leave, whereas middle-aged employees with longer work experience showed greater stability within the healthcare sector. Additionally, 76% of participants emphasized salary and incentives, 68% workplace atmosphere, and 73.3% opportunities for career advancement as key factors influencing job retention. Conclusion The study revealed that one in five healthcare workers intends to leave the healthcare sector, while one in four is considering leaving their current organization. Turnover intention varied significantly by age and profession.