We have developed a high performance atomic frequency standard based on Doppler-free direct frequency comb excitation of a two-photon transition in 87Rb. We demonstrate equivalent performance compared to an identical system based on cw laser excitation of the clock transition. This approach greatly simplifies optical clock architecture and eliminates the need for cw lasers in many two-photon frequency standards. The clock transition linewidth and ac-Stark shift measured directly with the frequency comb are shown to be nearly identical to those obtained using a cw laser of equal average power. We directly count this reference via the frequency comb repetition rate, achieving instabilities of 1.9 × 10-13 at 1 s averaging down to 7.8(38) × 10-15 at 2600 s, currently limited by temperature dependent shifts.