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Purpose: This study evaluates the effectiveness and impact of automated order-based protocol assignment for magnetic resonance imaging (MRI) exams using natural language processing (NLP) and deep learning (DL). Methods: NLP tools were applied to retrospectively process orders from over 116,000 MRI exams with 200 unique sub-specialized protocols ("Local" protocol class). Separate DL models were trained on 70\% of the processed data for "Local" protocols as well as 93 American College of Radiology ("ACR") protocols and 48 "General" protocols. The DL Models were assessed in an "auto-protocoling (AP)" inference mode which returns the top recommendation and in a "clinical decision support (CDS)" inference mode which returns up to 10 protocols for radiologist review. The accuracy of each protocol recommendation was computed and analyzed based on the difference between the normalized output score of the corresponding neural net for the top two recommendations. Results: The top predicted protocol in AP mode was correct for 82.8%, 73.8%, and 69.3% of the test cases for "General", "ACR", and "Local" protocol classes, respectively. Higher levels of accuracy over 96% were obtained for all protocol classes in CDS mode. However, at current validation performance levels, the proposed models offer modest, positive, financial impact on large-scale imaging networks. Conclusions: DL-based protocol automation is feasible and can be tuned to route substantial fractions of exams for auto-protocoling, with higher accuracy with more general protocols. Economic analyses of the tested algorithms indicate that improved algorithm performance is required to yield a practical exam auto-protocoling tool for sub-specialized imaging exams.