An automated pet door system. The system provides a user programmable database and system engine for controlling the passage of selected animals through a portal, such as a door, or screen, or other passage limiting device. The system is permissionable, in that the user may provide a set of dates, times, events, or other instructions, through a user input device to establish a then current operating envelope for each of one or more selected animals. A unique identification tag, which may use active radio frequency identification tag techniques, provides identity information for each candidate animal. Multiple sensor inputs, providing information such as door position, proximity of animals to the door, and direction and velocity of animals, are provided as inputs to a decision engine, which evaluates sensor inputs over time, before determining whether to open or close the pet door.