Background The World Health Organization recommended the Test, Treat and Track (T3) strategy for malaria control that, every suspected malaria case should be tested prior to treatment with Artemisinin-based combination therapy (ACT) and tracked. We assessed the performance and challenges in the implementation of T3 strategy among children under-five years in Volta and Oti Regions of Ghana. Method A descriptive cross-sectional study was carried in 69 health facilities. Exit interviews were conducted for caregivers of children with fever using a semi-structured questionnaire. Clinicians were interviewed at the out-patient department in each facility. Descriptive statistics was conducted, Chi-square test and logistic regression were used to determine the associations between completion of T3 and independent variables. Results Most children, 818/900 (90.9%) were tested for malaria and 600/818 (73.4%) were positive for malaria parasitaemia using rapid diagnostic test. Of those testing positive for malaria, 530/600 (88.3%) received treatment with ACTs. Half, (109/218) of the children testing negative for malaria also received ACTs. Also, 67/82 (81.7%) of children not tested for malaria received ACTs. Only 408/900 (45.3%) children completed T3 with Community Health-based Planning Services (CHPS) compound having the highest completion rate 202/314 (64.3%). CHPS Compounds were 6.55 times more likely to complete T3 compared to the hospitals [(95% CI: 3.77, 11.35), p<0.001]. Health facilities with laboratory services were 2.08 times more likely to complete T3 [(95% CI: 1.55, 2.79), p<0.001] The main challenge identified was clinicians’ perception that RDTs do not give accurate results. Conclusion Testing fever cases for malaria before treatment and treating positive cases with ACTs was high. Treating negative cases and those not tested with ACTs was also high. Health facilities having laboratory services and facility being CHPS compounds were key predictors of completing T3. Clinician’s not trusting RDT results can affect the T3 strategy in malaria control. Periodic training/monitoring is required to sustain adherence to the strategy.