School counselors are responsible for the well-being of students’ increasingly complex issues. However, little is known about school counseling services in the Kingdom of Bhutan. This study carried out 28 qualitative semi-structured interviews with school counselors, 19 online and 9 in-person, to investigate school counselors’ perceived challenges and resources. The data were analyzed using a phenomenological approach to inquiry and thematic analysis of interviews proposed by Braun and Clarke (2006). The identified challenges and resources were grouped for further analysis according to Martin et al. (2015) model of 11 factors affecting school counseling. The most often mentioned challenges were insufficient resources to cope with rising mental health needs (28; 100%) and cultural barriers to implementation of school counseling (26; 92.9%) such as stigma and role of corporal punishment. The most often mentioned resources were the importance of material resources such as having a separate counseling room within the school (n = 16; 57.1%) and the importance of support from external professionals such as clinical counselors (n = 11; 39.3%). In sum, the results revealed the needs for (1) more resources to cope with the various mental health needs of students across regions, (2) more awareness in the general population about school counseling, including overcoming stigma towards mental health, (3) to systemize stakeholder collaboration such that it make school counselor roles more clear, and (4) for more time for this profession to establish itself in the Kingdom.