A new control system for the Pegasus Thomson scattering diagnostic has recently been deployed to automate the laser operation, data collection process, and interface with the system-wide Pegasus control code. Automation has been extended to areas outside of data collection, such as manipulation of beamline cameras and remotely controlled turning mirror actuators to enable intra-shot beam alignment. Additionally, the system has been upgraded with a set of fast (∼1 ms) mechanical shutters to mitigate contamination from background light. Modification and automation of the Thomson system have improved both data quality and diagnostic reliability.