A thickness estimating apparatus includes a transfer robot, a light source, a camera, a memory and a controller. The memory stores a thickness predicting model generated based on a data set including a thickness of at least one of a test wafer corresponding to the wafer or a test element layer formed on the test wafer, and the thickness predicting model being trained to minimize a loss function of the data set. The controller applies pixel data, which is acquired from at least one pixel selected from a plurality of pixels included in a captured image, to the thickness predicting model, to predict a thickness of at least one of the wafer or an element layer formed on the wafer in a position corresponding to a position of the selected pixel.