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Electric power substations are experiencing an accelerated pace of digital transformation including the deployment of LAN-based IEC 61850 communication protocols that facilitate accessibility to substation data while also increasing remote access points and exposure to complex cyberattacks. In this environment, machine learning algorithms will play a vital role in cyberattack detection and mitigation and natural questions arise as to the most effective models in the context of smart grid substations. This paper compares the performance of three autoencoder-based anomaly detection systems including linear, fully connected, and convolutional autoencoders, as well as long short-term memory (LSTM) neural network for cybersecurity enhancement of transformer protection. The simulation results indicated that the LSTM model outperforms the other models for detecting cyberattacks targeting asymmetrical fault data. The linear autoencoder, fully connected autoencoder and 1D CNN further outperform the LSTM model for detecting cyberattacks targeting the symmetrical fault data.