As one of the fastest-growing technologies over the past half century, integrated circuit (IC) packaging is getting smaller and more complex. For example, typical silicon wafers in modern IC packaging have thicknesses ranging from several to tens of micrometers, and their coating layers are in the range of a few nanometers. Because the silicon wafer is the main substrate in IC packaging, it is important to accurately measure the geometry of a silicon wafer, especially its coating thickness, for process monitoring and quality control. In this study, an ultrafast ultrasonic measurement system is developed using a femtosecond laser for silicon wafer coating thickness estimation. The proposed technique provides the following unique features: (1) an ultrafast ultrasonic measurement system using a femtosecond laser is developed specifically for silicon wafer coating thickness estimation; (2) the developed system can estimate the thickness of a coating layer in the range of sub-micrometer; (3) except for the wave speed in the coating material, coating thickness can be estimated without any other prior knowledge of the coating material properties or substrate characteristics such as optical constants; and (4) the thermal effects on the ultrasonic waves propagating within a thin coating layer are explicitly considered and minimized for coating thickness estimation. Using the developed system, validation tests were successfully performed on gold-coated silicon wafers with different coating thicknesses.