The World Health Organization (WHO) staging is a commonly used rationing mechanism for highly active antiretroviral therapy (HAART)among various HIV infected populations including youths in most developing countries. Rationing is defined as any policy or practice that restricts consumption of or access to certain goods due to its limited supply. However, as HIV prevalence is rapidly increasing among youth, understanding the capacity of the staging approach to achieve HAART uptake in youth is of considerable importance. Aim This study aimed to explore how HAART rationing and access mechanisms impact on youth’s utilization of HAART in Malawi Methods The study used mixed methods with quantitative analysis of existing Ministry of Health Clinical HIV Unit data used to determine existing levels of youth HAART use. Qualitative methods employed in-depth interviews that interviewed nine ART providers, nine HIV positive youth on HAART and nine HIV positive youth not on HAART; and field observations to nine ART clinics were used to understand HAART rationing and access mechanisms and how such mechanisms impact youth uptake of HAART. Results The findings revealed that ART providers use both explicit rationing mechanisms like WHO clinical staging and implicit rationing mechanisms like use of waiting lists, queues and referral in ART provision. However, the WHO staging approach had some challenges in its implementation. It was also observed that factors like non-comprehensive approach to HAART provision, costs incurred to access HAART, negative beliefs and misconceptions about HAART and HIV were among the key factors that limit youth access to HAART. Conclusion The study recommends that while WHO staging is successful as a rationing mechanism in Malawi, measures should be put in place to improve access to CD4 assessment for clients who may need it. ART providers also need to be made aware of the implicit rationing mechanisms that may affect HAART access. There is also need to improve monitoring of those HIV positive youth not on HAART in order for the system to be able to commence them on treatment on time. Additionally, ART programmes need to address individual, programme and structural/social factors that may affect t youth’s access to HAART.