The present disclosure relates to a solid-state image sensor, an electronic apparatus and an imaging method by which specific processing other than normal processing can be sped up with reduced power consumption.The solid-state image sensor includes a pixel outputting a pixel signal used to construct an image and a logic circuit driving the pixel, and is configured of a stacked structure in which a first semiconductor substrate including a plurality of the pixels and a second semiconductor substrate including the logic circuit are joined together. In addition, among the plurality of pixels, a specific pixel is connected to the logic circuit independently of a normal pixel, the specific pixel being the pixel that outputs the pixel signal used in the specific processing other than imaging processing in which the image is imaged. The present technology can be applied to a stacked solid-state image sensor, for example.