The present technology relates to an imaging element, a method of manufacturing the imaging element, and an electronic apparatus that make it possible to suppress generation of a void in an infrared cutoff filter layer. The imaging element includes: a light receiving sensor that performs photoelectric conversion of incoming light; a cover glass that protects a top surface side serving as a light incidence surface of the light receiving sensor; a frame that is disposed in an outer peripheral portion between the light receiving sensor and the cover glass, and is formed with use of an inorganic material; and an infrared cutoff filter layer that is formed on an inner side on a same plane as the frame. The present technology is applicable to, for example, an imaging element having a CSP structure, and the like.