The human retina contains long [L]-wavelength, medium [M]-wavelength, and short [S]-wavelength cones, rods, and intrinsically photosensitive retinal ganglion cells expressing the blue-sensitive (λmax = ~480 nm) photopigment melanopsin. Previous animal studies have pointed to a role of melanopsin in advancing circadian phase, melatonin suppression, the pupillary light reflex (PLR), light avoidance, and brightness discrimination, often relying on genetic tools to study melanopsin in isolation in animal models. This work addresses the question of human melanopsin sensitivity and function in vivo using a spectrally tunable light source and the method of silent substitution, allowing for the selective stimulation of melanopsin in the human retina, in combination of pupillometry, psychophysics, and BOLD functional neuroimaging (fMRI). In three studies, we find (1) that the temporal transfer function of melanopsin in controlling the pupil in humans is low-pass, peaking at slow temporal frequencies (0.01 Hz), with a sharp drop off at higher frequencies (1-2 Hz); (2) that signals originating from S cones get combined in an antagonistic fashion with melanopsin signals and signals from L and M cones cones, demonstrating spectral opponency in the control of the human PLR; (3) that nominally cone-silent melanopsin-directed spectral modulations stimulate cones in the partial shadow of the retinal blood vessels (termed penumbral cones), leading to the entoptic percept of the subjective retinal vasculature; and (4) that there is no measurable signal due to melanopsin stimulation in human visual cortical areas (V1, V2/V3, MT, LOC; measured with BOLD fMRI) at temporal frequencies most relevant to spatial vision (0.5–64 Hz) while modulations directed at L+M, L–M and S photoreceptor combinations yield characteristic temporal transfer functions in these areas. This work advances to our understanding of the functional significance of melanopsin function in the human visual system, contributing to the study of human health in relation to light and color.