A correct protocol assignment is critical to high-quality imaging examinations, and its automation can be amenable to natural language processing (NLP). Assigning protocols for abdominal imaging CT scans is particularly challenging given the multiple organ specific indications and parameters. We compared conventional machine learning, deep learning, and automated machine learning builder workflows for this multiclass text classification task. A total of 94,501 CT studies performed over 4 years and their assigned protocols were obtained. Text data associated with each study including the ordering provider generated free text study indication and ICD codes were used for NLP analysis and protocol class prediction. The data was classified into one of 11 abdominal CT protocol classes before and after augmentations used to account for imbalances in the class sample sizes. Four machine learning (ML) algorithms, one deep learning algorithm, and an automated machine learning (AutoML) builder were used for the multilabel classification task: Random Forest (RF), Tree Ensemble (TE), Gradient Boosted Tree (GBT), multi-layer perceptron (MLP), Universal Language Model Fine-tuning (ULMFiT), and Google’s AutoML builder (Alphabet, Inc., Mountain View, CA), respectively. On the unbalanced dataset, the manually coded algorithms all performed similarly with F1 scores of 0.811 for RF, 0.813 for TE, 0.813 for GBT, 0.828 for MLP, and 0.847 for ULMFiT. The AutoML builder performed better with a F1 score of 0.854. On the balanced dataset, the tree ensemble machine learning algorithm performed the best with an F1 score of 0.803 and a Cohen’s kappa of 0.612. AutoML methods took a longer time for completion of NLP model training and evaluation, 4 h and 45 min compared to an average of 51 min for manual methods. Machine learning and natural language processing can be used for the complex multiclass classification task of abdominal imaging CT scan protocol assignment.