Cervical cancer is one of the leading causes of cancer deaths among women in low- and middle-income countries such as South Africa. The current impact of national cervical cancer control and sexual and reproductive health interventions in South Africa reduce its burden. The aim of this study was to assess the trends in cervical cancer mortality and its relation to breast and gynaecological cancers in South Africa from 1999 to 2018. We conducted joinpoint regression analyses of the trends in crude and age-standardised mortality rates (ASMR) for cervical cancer mortality in South Africa from 1999 to 2018. An age–period–cohort regression analysis was also conducted to determine the impact of age, period, and cohort on cervical cancer mortality trends. Analyses were stratified by ethnicity. Cervical cancer (n = 59,190, 43.92%, 95% CI: 43.65–44.18%) was responsible for about 43.9% of breast and gynecological cancer deaths. The mortality rate of cervical cancer (from 11.7 to 14.08 per 100,000) increased at about 0.9% per annum (Average Annual Percent Change (AAPC): 0.9% (AAPC: 0.9%, p-value < 0.001)), and young women aged 25 to 49 years (AAPC: 1.2–3.5%, p-value < 0.001) had increased rates. The risk of cervical cancer mortality increased among successive birth cohorts. In 2018, cervical cancer mortality rate among Blacks (16.74 per 100,000 women) was about twice the rates among Coloureds (8.53 deaths per 100,000 women) and approximately four-fold among Indians/Asians (4.16 deaths per 100,000 women), and Whites (3.06 deaths per 100,000 women). Cervical cancer control efforts should be enhanced in South Africa and targeted at ethnic difference, age, period, and cohort effects.