Background Isthmocele or a scar defect is a relatively common consequence of cesarean section resulting in menstrual disturbances and infertility and may compromise the myometrial integrity of the uterus in women contemplating subsequent vaginal birth. Several preventive measures have been suggested, including the modification of surgical techniques used for the closure of the uterine incision. The current study aimed to compare the incidence of isthmocele and assess residual myometrial thickness in women who underwent single versus parallel layered closure to approximate the endo-myometrial layer during cesarean section. Methodology This retrospective study evaluated data of women undergoing their first cesarean section under elective conditions (n = 497) where the uterine incision was closed using a single (n = 295) or a parallel layer (n = 202) technique. Patients were evaluated twice, at 3-6 months and 18 months postpartum, with a transvaginal ultrasound noting the presence or absence of an isthmocele and measurement of the residual myometrial thickness. Results Regardless of the closure technique, 64 (12.9%) women had an ultrasound-diagnosed isthmocele. Significantly fewer patients in the parallel-layer closure group presented with an isthmocele both at 3-6 (13.6 vs. 6.9%; p = 0.019) and 18 months (16.3 vs. 7.8%; p = 0.009) postpartum. Residual myometrium was significantly thicker in the parallel-layer closure group (8.0 vs. 13.2 mm at 3-6 months postpartum; p = 0.000 and 7.2 vs. 12.3 mm at 18 months postpartum; p = 0.004). For all patients, a retroverted position of the uterus at 3-6 months follow-up examination significantly increased the frequency of isthmocele (36/395 (9.1%) with an anteverted uterus and 18/102 (17.6%) with a retroverted uterus; p = 0.002). In patients with a single-layer closure, a retroverted uterus at the 3-6-month follow-up was associated with an isthmocele in 29.5% (18/61) of patients, while no isthmocele was recorded when the uterus was retroverted in the parallel-layer closure group (0/41) (p = 0.001). At 18 months postpartum, of the 64 patients with an isthmocele, 26 (40.6%) presented with abnormal uterine bleeding mainly in the form of postmenstrual spotting. Of the 26 patients with abnormal bleeding, 23 were in the single-layer and three were in the parallel-layer closure group. Conclusions The parallel-layer closure when compared to a single-layer closure of the uterine incision in patients undergoing primary cesarean section decreased the incidence of isthmocele formation and increased residual myometrial thickness. More patients in the single-layer closure group had menstrual cycle disturbances at 18 months postpartum.