Introduction Radiotherapy plays a vital role in the management of gynecological malignancies. However, maintaining patient position poses a challenge during daily radiotherapy treatment of these patients. This study identifies and calculates setup errors in interfraction radiotherapy and optimum clinical target volume-planning target volume (CTV-PTV) margins in patients with gynecological malignancies. Material and methods A total of 38 patients with gynecological malignancies were included in the study. They were treated with a dose of 50 Gy in 25 fractions for five weeks, followed by brachytherapy. All patients were immobilized using a 4-point thermoplastic cast. Anteroposterior and lateral images were taken thrice weekly for five weeks. Setup verification was done using kilovoltage images obtained using Varian On-board Imager (Varian Medical System, Inc., Palo Alto, CA). Manual matching was done utilizing bony landmarks such as the widest portion of the pelvic brim, anterior border of S1 vertebrae, and pubic symphysis in the X, Y, and Z axes, respectively. Results A total of 1140 images were taken. The individual systematic errors ranged from -0.24 to 0.17 cm (LR), -0.15 to 0.19 cm (AP) and -0.36 to 0.29 cm (CC) while the individual random errors ranged from 0.04 to 0.36 cm (LR), 0.06 to 0.33 cm (AP) and 0.10 to 0.29 cm (CC). The calculated CTV-PTV margins in LR, AP and CC directions were 0.17, 0.18, and 0.25 cm (ICRU-62); 0.28, 0.31 and 0.47 cm in LR, AP and CC directions (Stroom's), and 0.32, 0.36 and 0.55 cm (Van Herk) respectively. Conclusion Based on this study, the calculated CTV-PTV margin is 6 mm in gynecological malignancies, and the present protocol of 7 mm of PTV margin is optimum.