Ectopic pregnancies (EPs) are potentially fatal if not recognized early. Evidence of an association with chlamydial infection in South East Asia is lacking. This case-control study aims to (i) compare chlamydial infection in women with EP to women who delivered a full-term pregnancy, (ii) investigate classical factors associated with EP, and (iii) investigate rupture status in EP. Seventy-two women with a confirmed diagnosis of EP and sixty-nine who delivered a full-term pregnancy in a tertiary hospital in Malaysia were recruited from November 2019 to January 2022. Demographic and relevant clinical data and intraoperative findings were documented. Blood samples for testing IgG levels of chlamydia were obtained. Women with EP were more likely to have tested positive for chlamydia than those with a full-term delivery (34.7% vs. 13.0%, AOR = 4.18, 95% CI = 1.67–10.48, p = 0.002). The majority did not have the classic risk factors associated with EP. An amount of 52.8% presented with a ruptured EP, with 84.2% of ruptures occurring after six weeks of gestation. An amount of 44.2% had an estimated blood loss of more than 500 cc, with 20% losing more than 1500 cc of blood. The prevalence of prior chlamydial infection in women with EP is significant enough to necessitate a review of early pregnancy care.