We consider the problem of calibration and uncertainty analysis for activity-based transportation simulators. Activity-Based Models (ABMs) rely on statistical modeling of individual travelers' behavior to predict higher-order travel patterns in metropolitan areas. Input parameters are typically estimated from traveler surveys using maximum likelihood. We develop an approach that uses a Gaussian Process emulator to calibrate those parameters using traffic flow data. Our approach extends traditional emulators to handle the high-dimensional and non-stationary nature of transportation simulators. We introduce a deep learning dimensionality reduction model that is jointly estimated with Gaussin Process model to approximate the simulator. We demonstrate the methodology using several simulated examples as well as by calibrating key parameters of the Bloomington, Illinois model.