Gas Metal Arc Welding (GMAW) is one of the main methods used to join structural members. One of the largest challenges involved in production of welds is ensuring the quality of the weld. One of the main factors attributing to weld quality is penetration depth. Automatic control of the welding process requires non-contact, non-destructive sensors that can operate in the presence of high temperatures and electrical noise found in the welding environment. Inspection using laser generation and electromagnetic acoustic transducer (EMAT) reception of ultrasound was found to satisfy these conditions. Using this technique, the time of flight of the ultrasonic wave is measured and used to calculate penetration depth. Previous works have shown that penetration depth measurement performance is drastically reduced when performed during welding. This work seeks to realize in-process penetration depth measurement by compensating for errors caused by elevated temperature. Neuro-fuzzy models are developed that predict penetration depth based on in-process time of flight measurements and the welding process input. Two scenarios are considered in which destructive penetration depth measurements are or are not available for model training. Results show the two scenarios are successful. When destructive measurements are unavailable, model error is comparable to that of offline ultrasonic measurements. When destructive measurements are available, measurement error is reduced by 50% compared to offline ultrasonic measurements. The two models can be effectively applied to permit in-process penetration depth measurements for the purpose of real-time monitoring and control. This will reduce material, production time, and labor costs and increase the quality of welded parts.