Background Intimate partner violence (IPV) violence is an important public health problem with negative long term effects on the mother’s health and the unborn baby. In one Namibian study performed in the capital city over one third (36%) of ever-partnered women reported physical or sexual violence from an intimate partner. No study had been conducted to determine the prevalence of IPV amongst pregnant women in a primary care setting in Namibia. Aim and objectives This study aimed to determine the prevalence of IPV amongst women attending antenatal care at Outapi primary health care clinic, Namibia. The objectives of the study were to measure the prevalence of IPV amongst pregnant women, to assess the relationship between the different types of IPV and to evaluate the presence of known risk factors for IPV. Methods A descriptive survey conducted at Outapi clinic in Namibia. Data was collected using a validated questionnaire from 386 consecutive participants in the antenatal clinic. Results The mean age of the participants was 27.5 years (SD 6.8) and 335(86.8%) of the women were unmarried, 215(55.7%) with only primary school education and 237(61.4%) in their third trimester. Overall 41(10.6%) had HIV and 44(11.4%) were teenage pregnancies. The reported lifetime prevalence of IPV was 10.1%, the 12-month prevalence was 27(7.0%) and the prevalence during pregnancy was 23(6.0%). Emotional abuse was the commonest type of abuse in 27(7.0%) although the commonest specific abusive behaviour was refusing to provide money to run the house or look after the children when there was money for other things in 19(4.9%). Increased age was associated with an increase in occurrence of IPV. Conclusion Presence of IPV in this setting is comparable to Uganda and Malawi but much less than prevalence in neighbouring countries. Nevertheless, the prevalence is sufficient to warrant the development of guidelines to recognize, assess and assist women affected by IPV.