Aim To evaluate the clinical factors associated with false-negative RT-PCR results and to report the outcome of a cohort of pregnant women with COVID-19. Methods This cohort study was conducted in a tertiary referral pandemic hospital and included 56 pregnant women. A study including pregnant women with either a laboratory or clinical diagnosis for COVID-19 were included in the study. The primary outcome was clinical factors associated with false-negative RT-PCR results defined as a positive immunoglobulin M assessed by rapid testing in clinically diagnosed patients. Clinical outcomes of laboratory diagnosed patients were also reported. Results In total, 56 women with either RT-PCR or clinical COVID-19 diagnosis were included in the study. Forty-three women either had RT-PCR positivity or IgM positivity. The clinical outcome of these pregnancies was as follows: mean maternal age 27.7, immunoglobulin M positive patients 76.7%, RT-PCR positive patients 55.8%, maternal comorbidities 11.5%, complications in patients below 20 weeks 34.8%, complications in patients above 20 weeks 65.1%, elevated CRP 83.7%, lymphopenia 30.2%, time from hospital admission to final follow-up days 37 and stillbirth 8.3%. The proportion of women who tested positive for SARS-CoV-2 immunoglobulin M was 100% in the RT-PCR positive group and 56.5% in the clinical diagnosis group (P = .002). The symptom onset to RT-PCR testing interval longer than a week (risk ratio: 2.72, 95% CI: 1.14-5.40, P = .003) and presence of dyspnoea (risk ratio: 0.38, 95% CI: 0.14-0.89, P = .035) were associated with false-negative RT-PCR tests. The area under the curve of these parameters predicting false-negative RT-PCR was 0.73 (95% CI: 0.57-0.89). Conclusions Symptomatic women with a negative RT-PCR should not be dismissed as potential COVID-19 patients, especially in the presence of prolonged symptom onset-test interval and in women without dyspnoea.