In a method of operating a depth pixel included in a three-dimensional (3D) image sensor, a plurality of sampling values are obtained by sampling a reception light reflected by an object based on a transfer control signal having a first initial activation level. The depth pixel includes a photo detection region, a transfer gate and a floating diffusion region. The transfer control signal is applied to the transfer gate. A first final activation level of the transfer control signal is determined based on the plurality of sampling values and at least one reference value. A distance between the depth pixel and the object is calculated based on the reception light and the transfer control signal having the first final activation level.