The COVID-19 pandemic has had severe and potentially long-lasting impacts on the South African economy since the onset of the national lockdown in March 2020. These effects have not been equally distributed. Employment effects have been disproportionately felt by several vulnerable groups, including women. However, few authors have examined the outcomes of those who retained their jobs, especially in developing countries. In this light, this paper uses new representative survey data to investigate whether gender wage inequality has deepened among job retainers in South Africa. We estimate the conditional and unconditional gender wage gaps at the mean, showing that women earned 29% less than men per hour prior to South Africa’s national lockdown, expanding to 43% less during June 2020. We proceed to use Recentred Influence Function (RIF) regressions to estimate the gender wage gap across the wage distribution given evidence of heterogeneity in South Africa. We find that the gap exists at almost all points of the distribution in both periods, but it has deepened significantly amongst the poorest 40% of earners. This finding is robust to a reweighting sample selection correction. We argue that this increased wage inequality was driven by a reduction in working hours amongst women relative to men due to an increased childcare burden during the lockdown.