We present the first demonstration of shot-noise limited supercontinuum-based spectral domain optical coherence tomography (SD-OCT) with an axial resolution of 5.9 μm at a center wavelength of 1370 nm. Current supercontinuum-based SD-OCT systems cannot be operated in the shot-noise limited detection regime because of severe pulse-to-pulse relative intensity noise of the supercontinuum source. To overcome this disadvantage, we have developed a low-noise supercontinuum source based on an all-normal dispersion (ANDi) fiber, pumped by a femtosecond laser. The noise performance of our 90 MHz ANDi fiber-based supercontinuum source is compared to that of two commercial sources operating at 80 and 320 MHz repetition rate. We show that the low-noise of the ANDi fiber-based supercontinuum source improves the OCT images significantly in terms of both higher contrast, better sensitivity, and improved penetration. From SD-OCT imaging of skin, retina, and multilayer stacks we conclude that supercontinuum-based SD-OCT can enter the domain of shot-noise limited detection.