The consumption of fossil fuel significantly contributes to the growth of South Africa’s economy but produces carbon dioxide (CO2), which is detrimental to environmental sustainability with overall effects on health outcomes. This study sought to (i) examine the impacts of fossil energy consumption-related CO2 emissions on the under-five mortality and infant mortality rates in South Africa and (ii) analyse the causal relationship between fossil energy consumption, CO2 emissions, and mortality rates in South Africa. Linear and nonlinear ARDL bounds and the Toda–Yamamoto causality test were used to establish the equilibrium property in the long run and the causal effects of the models’ variables. Health outcome data include the under-five mortality rate (MTR1) and infant mortality rate (MTR2). Other explanatory variables include fossil energy consumption (FOC), inflation (Inf), carbon dioxide emissions (CO2), and government expenditure (GEH). It is evident from the results of linear ARDL that the first lag of the under-five mortality rate in the short run has a positive and significant impact on the under-five mortality rate in South Africa. Holding the other variables constant, the under-five mortality rate in South Africa would increase by 0.630% for every 1% increase in its lagged values. Fossil energy consumption has a positive and significant effect on the under-five mortality rate in South Africa. This significant relationship implies that a 1% increase in fossil energy consumption increases the under-five mortality rate per 1000 persons per year in South Africa by 0.418% in the short run, all things being equal. The results from the Toda–Yamamoto causality test revealed that there is no causality between the under-five mortality rate and both the consumption of fossil fuel and CO2 emissions in South Africa. The results from nonlinear ARDL presented four separate scenarios. In the short run, during increasing levels of CO2 in the initial period (lag of CO2), a 1% increase in CO2 would decrease the under-five mortality rate by 1.15%. During periods of decreasing levels of CO2 in the short run, a 1% increase in CO2 would increase the infant mortality rate by 0.66%. Again, during previous and current periods of decreasing levels of FEC, a 1% increase in FEC would increase the infant mortality rate by 0.45% and 0.32%, respectively. In the long run, during periods of increasing levels of CO2, a 1% increase in CO2 would decrease the infant mortality rate by 4.62% whereas during decreasing levels of CO2, a 1% increase in CO2 would increase the infant mortality rate by 2.3%. The risk posed by CO2 emissions and their effects on humans can then be minimised through a government expansionary policy within health programmes.