SSZ-13 and SSZ-39 zeolites were synthesized, then were with Cu ion-exchanged to obtain catalysts with similar Cu content and tested during NO selective catalytic reduction with NH3 (NH3-SCR), in order to investigate the effect of two zeolites with similar structures in NH3-SCR. Both catalysts were very active in the 150–600 °C temperature range. It was necessary to use high space velocity (520,000 h−1) to properly determine the activity during NH3-SCR of our catalysts in the 150–600 °C temperature range. At higher space velocity, a complete picture of the reactivity of each catalyst was revealed. The 2.5/SSZ-13 catalyst was observed to have a higher NO activity per Cu than 3.7/SZZ-39. The conversion-temperature traces were different, with a “Seagull shape” present in the 3.7/SSZ-39 catalyst. This difference seems to be linked to variations in the Cu exchange level and the distribution of Cu species between both zeolitic structures. The activation energy and preexponential factors calculated assuming a pseudo-first-order reaction during SCR start were also different, presumably reflecting minor variations in the active Cu-zeolite bonding. Measurements by TPD- NH3 gave a similar amount of NH3 adsorbed in both materials (~ 0.14 mmol NH3/g), but the temperature at the maximum desorption rate was different (430 °C-2.5/SSZ-13 and 290 °C-3.7/SSZ-39); this is related to differences in Cu content. Our UV–VIS-NIR data show variations in the distribution of Cu species because of the reaction. Dimeric Cu sites and Cu2+ were significant in both catalysts after the reaction. The Cu content and the structure of the active Cu sites are significant factors determining the activity variations as a function of temperature and in understanding the activity of these small pore zeolites.