Abstract: A system and a method are disclosed for estimating a latency of a layer of a neural network. A host processing device adds an auxiliary layer to a selected layer of the neural network. A neural processing unit executes an inference operation over the selected layer and the auxiliary layer. A total latency is measured for the inference operation for the selected layer and the auxiliary layer, and an overhead latency is measured for the inference operation. The overhead latency is subtracted from the total latency to generate an estimate of the latency of the layer. In one embodiment, measuring the overhead latency for the inference operation that is associated with the auxiliary layer involves modeling the overhead latency based on a linear regression of an input data size that is input to the selected layer, and an output data size that is output from the auxiliary layer.