Heat-affected zones (HAZs) of Inconel 939 (IN-939) superalloy are susceptible to cracking during welding process. Preventing cracking during the repair welding of turbine components is important. In this study, the effects of heat input and pre-welding heat treatment on the microstructure, mechanical properties and crack formation in tungsten inert gas welding of IN-939 were investigated. The whole specimens were welded using Inconel 625 filler in an Ar atmosphere and characterised by metallographic examinations and hardness measurements. Results showed that the microstructures of IN-939 HAZs were highly susceptible to cracking during welding due to increasing of γ′ volume fraction. All of these cracks appeared in the HAZs and grew perpendicular to the melting zone along the grain boundaries. In this survey, the pre-welding heat treatment and heat input strongly affected the HAZ microstructure and hardness. However, the pre-welding heat treatment with 67% impact was more effective than heat input with 30% impact. Finally, hot tensile tests were carried out on the specimens of the base metal and the optimal specimens under similar operating conditions within 600 °C–800 °C. Welding process did not affect the yield strength of the superalloy but slightly decreased its ultimate strength and elongation by as much as 92% and 50%, respectively, of those of the base metal.