The ordering of protons has been observed at a new storage ring, S-LSR, at Kyoto University. Abrupt jumps in the momentum spread and the Schottky noise power were observed for protons for the first time at a particle number of approximately 2000, upon applying electron cooling with electron currents of 25, 50, and 100 mA. The transition temperature was 0.17 and 1 meV in the longitudinal and transverse directions, respectively. The transverse temperature of the proton beam was much below that of electrons at the transition, which played an essential role in the ordering of protons.