Currently, surgical treatment aimed to exclude the malignant ovarian tumors is performed in almost 90% of patients with decidualized endometrial cysts (DEC). However, unnecessary surgical interventions increase the risk to maternal and fetal health. The study was aimed to perform a differential diagnosis of DEC in pregnant women in order to define the rational treatment. A total of 82 female patients were included in the study: 63 had endometrial cysts (EC), 16 had DEC, 3 had rare forms of endometriosis, and 10 had ovarian serous papillary borderline tumors. When performing the diagnostic ultrasound, our proposed model was used. The ultrasound imaging data obtained were juxtaposed with the concentration of the protein tumor markers (СА-125), the risk of malignancy index (RMI) was calculated, and the morphological assessment of the masses was performed. The ultrasound imaging parameters, being the most valuable for differential diagnosis of EC, DEC, and serous borderline tumors, were as follows: the altered mass wall thickness, the existence and shape of papillary masses, avascular echogenic inclusions with blurry contour, blood circulation and arrangement of blood vessels, ascites. The frequency analysis revealed the differences between groups based on the ultrasound imaging data (in 60–100% of observations). Histological examination revealed the differences between groups in 100% of observations. Our findings have made it impossible to prolong pregnancy in patients with DEC without performing surgery. The results of treatment provided to patients with DEC during pregnancy were worse compared to those in patients with no prominent decidualization in ovarian EC. Today, the diagnosis of DEC and the treatment of patients during pregnancy remain unsophisticated. Further clinical observation and the search for more reliable methods of the diagnosis and rational treatment of pregnant women with DEC are required.