BACKGROUND Long waiting times are a major source of dissatisfaction for patients attending public healthcare facilities in South Africa (SA). The National Department of Health has identified this as one of six priority areas for improvement. Health system-strengthening (HSS) interventions to improve patient waiting time are being implemented in public health facilities across SA as part of the 'Ideal Clinic' model. The effect of these interventions on patient waiting time needs to be assessed and evidence generated for system improvement. OBJECTIVE To determine the effect of Ideal Clinic HSS intervention on patient waiting time in public health facilities in Amajuba District, KwaZulu-Natal Province, SA. METHODS We implemented 12 months of HSS activity, including facility reorganisation and patient appointment scheduling. The major outcome of interest was the total time spent by patients in a facility during a visit. This was calculated as the median time spent, obtained through a 'before-and-after' intervention survey. Univariate and multivariate factors associated with waiting time were determined. RESULTS A total of 1 763 patients from nine clinics were surveyed before and after the intervention (n=860 at baseline and n=903 at follow-up). The median overall waiting time after the intervention was 122 minutes (interquartile range (IQR) 81 - 204), compared with 116 minutes (IQR 66 - 168) before (p<0.05). Individual facility results after the intervention were mixed. Two facilities recorded statistically significant reductions in patient waiting time, while three recorded significant increases (p<0.05). Patient load per nurse, type of service received and time of arrival in facilities were all independently associated with waiting time. Patients' arrival patterns, which were determined by appointment scheduling, played a significant role in the results obtained. CONCLUSIONS Implementation of the Ideal Clinic model in the selected facilities led to changes in patient waiting time. Observed changes were positive when a clinic appointment system was successfully implemented and negative when this was unsuccessful. We recommend strengthening of the appointment system component of the Ideal Clinic model to improve patient waiting time. Assessing facility waiting time performance in terms of average time spent by patients during a clinic visit was shown to be inadequate, and we suggest the inclusion of 'proportion of clients who spent above the national waiting time threshold during their visit' as a sensitive measure of performance.