This study aimed to develop and validate convolutional neural network (CNN) models for distinguishing follicular thyroid carcinoma (FTC) from follicular thyroid adenoma (FTA). Additionally, this current study compared the performance of CNN models with the American College of Radiology Thyroid Imaging Reporting and Data System (ACR-TIRADS) and Chinese Thyroid Imaging Reporting and Data System (C-TIRADS) ultrasound-based malignancy risk stratification systems. A total of 327 eligible patients with FTC and FTA who underwent preoperative thyroid ultrasound examination were retrospectively enrolled between August 2017, and August 2024. Patients were randomly assigned to a training cohort (n = 263) and a test cohort (n = 64) in an 8:2 ratio using stratified sampling. Five CNN models, including VGG16, ResNet101, MobileNetV2, ResNet152, and ResNet50, pre-trained with ImageNet, were developed and tested to distinguish FTC from FTA. The CNN models exhibited good performance, yielding areas under the receiver operating characteristic curve (AUC) ranging from 0.64 to 0.77. The ResNet152 model demonstrated the highest AUC (0.77; 95% CI, 0.67-0.87) for distinguishing between FTC and FTA. Decision curve and calibration curve analyses demonstrated the models' favorable clinical value and calibration. Furthermore, when comparing the performance of the developed models with that of the C-TIRADS and ACR-TIRADS systems, the models developed in this study demonstrated superior performance. This can potentially guide appropriate management of FTC in patients with follicular neoplasms.