BACKGROUND: Health care workers (HWs) support HIV positive children and adolescents with detectable HIV viral loads on the intensive adherence counselling (IAC) program to achieve viral suppression through individual adherence counselling. Low re-suppression rates of 23% showed low program effectiveness in fifteen public health facilities. OBJECTIVES: We set out to determine the knowledge and perceptions of HWs that support this program to improve its effectiveness. METHODS: We conducted a qualitative study where five HWs that oversee clinical care for children on ART were interviewed about the program. Data on their knowledge of the program, and perceptions on why it was not effective was collected. Thematic analysis using the inductive approach was used. Transcripts were read, coded and emergent themes determined. RESULTS: Five HWs participated and all were knowledgeable about the program. Two themes emerged as barriers to IAC program effectiveness, patient factors and health system factors. Patient factors were failure to attend appointments, failure to change adherence practices, and lack of consent. Health system factors were work overload, delay in getting results and drug stock outs. CONCLUSIONS: HWs are knowledgeable about the IAC program and client specific barriers should be addressed to improve viral suppression for children.