Abstract Background The impacts caused by COVID-19 on pregnant and postpartum women are not well characterized yet. It is well known that, due to pregnancy, the maternal organism undergoes immunological adaptations, which may increase the risk of complications of viral diseases. These adaptations, in addition to the inflammatory disorder caused by the SARS-Cov-2, may contribute to severe outcomes as a result of COVID-19 infection. In this study the peripheral levels of total T lymphocytes, CD4+ T lymphocytes, CD8+ T lymphocytes, B lymphocytes and natural killer cells in pregnant and postpartum women with positive and negative PCR for SARS-CoV-2 were determined. Methods A cross-sectional study was performed using peripheral blood samples from pregnant and postpartum women who underwent PCR for the diagnosis of COVID-19 between May 2021 and March 2022. Samples were collected in a public maternity hospital in Northeast of Brazil right on admission for delivery as well as in the immediate puerperium. Blood was collected in tubes containing EDTA for flow cytometry, using the activated cell fluorescence analyzer (FACScan) and the Cell Quest software. The total of T lymphocyte subsets (CD3+), CD3+/CD4+ (ThL) and CD3+/CD8+ (TcL) was determined according to published protocols. B lymphocytes were identified by expression of CD19 (CD19+) and NK and NKT cells were identified by the CD16+/56+ and CD3+/CD16-56+ phenotype, respectively. Lymphocytes were identified by high CD45 expression and low side scatter using the following 3-color monoclonal antibody combinations: fluorescein isothiocyanate (FITC), phycoerythrin (PE) and chlorophyll pyridine protein (PerCP). Results A total of 99 women with a mean age 29 (± 7) years old were used in this study, of which 31 (31.3%) were pregnant and 68 (69.4%) were postpartum women. The diagnosis of COVID-19 was confirmed by PCR in 78 (78.8%) of the participants and in 21 (21.2%) it was discarded after negative PCR. Pregnant and postpartum women infected with SARS-CoV-2 had higher levels of cytotoxic T cells, median (ME) = 574.2; interquartile range (IIQ) = 382.4, when compared with uninfected patients, ME = 404.7; IIQ = 363.5); P = 0.032. Pregnant women with COVID-19 had a lower mean CD3+ count (1351.1 ± 337.7) compared to postpartum women with the disease (1605.6 ± 538.6); t (53.6) = −2.45, P = 0.009. Likewise, lower CD16+/56+ (113.3; IIQ = 172.0) and CD3+/CD16-56+ (52.1; IQ = 53.4) medians were found in pregnant women with COVID-19, when compared with the group of postpartum women without infection (191.2; IIQ = 192.5); U = 396.0, P = 0.043 and (70.8; IIQ = 91.6); U = 376.5, P = 0.025, respectively. Conclusion Pregnant and postpartum women with COVID-19 had significantly higher levels of cytotoxic T cells in peripheral blood. These results may be useful to understand what the SARS-CoV-2 infection causes in the immune system of pregnant and postpartum women. On the other hand, observational studies with larger samples and bias control are required.