Introduction: An estimated 13% of women in the postnatal period suffer from postnatal depression (PND) worldwide. In addition to underprivileged women, women who are exposed to violence are at higher risk of PND. This study aimed to investigate the relationship between intimate partner violence (IPV) and PND in Malaysia. Methods: This survey was conducted as a nationwide cross-sectional study using a cluster sampling design. Probable PND was assessed using a self-administered Edinburgh Postnatal Depression Scale (EPDS). Demographic profiles and IPV were assessed using a locally validated WHO Multicountry Study on Women’s Health and Life Events Questionnaire that was administered in a face-to-face interview. An EPDS total score of 12 or more and/or a positive tendency to self-harm were used to define PND. Results: Out of 6669 women, 5727 respondents were successfully interviewed with a response rate of 85.9%. The prevalence of probable PND was 4.4% (95% CI 2.9 to 6.7). The overall prevalence of IPV was 4.9% (95% CI 3.8 to 6.4). Among the women in this group, 3.7% (95% CI 2.7 to 5.0), 2.6% (95% CI 1.9 to 3.5) and 1.2% (95% CI 0.9 to 1.7) experienced emotional, physical and sexual violence, respectively. Logistic regression analysis revealed that women who were exposed to IPV were at 2.3 times the risk for probable PND, with an adjusted OR (aOR) of 2.34 (95% CI 1.12 to 4.87). Other factors for PND were reported emotional violence (aOR 3.79, 95% CI 1.93 to 7.45), unplanned pregnancy (aOR 3.32, 95% CI 2.35 to 4.69), lack of family support during confinement (aOR 1.79, 95% CI 1.12 to 2.87), partner’s use of alcohol (aOR 1.59, 95% CI 1.07 to 2.35) or being from a household with a low income (aOR 2.99; 95% CI 1.63 to 5.49). Conclusions: Exposure to IPV was significantly associated with probable PND. Healthcare personnel should be trained to detect and manage both problems. An appropriate referral system and support should be made available.