Photoreceptors mediate the first step of vision, transducing light and passing signals to retinal neurons that ultimately send signals along the optic nerve to the brain. A functional deficiency in the photoreceptors, due to either congenital or acquired disease, can significantly affect an individual’s sight and quality of life. Methods for quantifying the health and function of photoreceptors are essential for understanding both the progression of disease and the efficacy of treatment. Given that emerging treatments such as gene, stem cell, and small molecule therapy are designed to operate at the cellular scale, it is desirable to monitor function at the commensurate resolution of individual photoreceptors. Previously, non-invasive imaging methods for visualizing photoreceptor mosaic structure have been used to infer photoreceptor health, but these methods do not assess function directly. Conversely, most functional techniques, such as ERG and conventional microperimetry, measure function by aggregating the effects of signals from many photoreceptors. We have previously shown that stimulus-evoked intrinsic changes in intensity can be measured reliably in populations of cone photoreceptors in the intact human eye, a measurement we refer to more generally as the cone optoretinogram. Here we report that we can resolve the intensity optoretinogram at the level of individual cones. Moreover, we show that the individual cone optoretinogram exhibits two key signatures expected of a functional measure. First, responses in individual cones increase systematically as a function of stimulus irradiance. Second, we can use the amplitude of the functional response to middle wavelength (545 nm) light to separate the population of short-wavelength-sensitive (S) cones from the population of middle- and long-wavelength-sensitive (L and M) cones. Our results demonstrate the promise of optoretinography as a direct diagnostic measure of individual cone function in the living human eye.