Kepler’s Gyr-old short-period exoplanet population provides key insights into planetary evolution, particularly the radius valley, which likely arises from atmospheric mass loss and/or migration timescales. To understand the nature of the primordial population, we must study planets in their youth. Using TESS, we investigate short-period (<12 days), Neptune-sized planets (1.8–10 R⊕) orbiting 1374 FGK stars in nearby (<200 pc), young clusters (<1 Gyr). We find that the occurrence rate of young close-in Neptunes is 2–3 times higher than that of their Gyr-old Kepler counterparts, a difference not predicted by current formation and evolution models. By separating the sample into 10–100 Myr and 100 Myr–1 Gyr bins, we observe a stable orbital period distribution over time, but a steepening radius distribution — likely due to atmospheric cooling and mass loss. We also find a possible increase in occurrence after 100 Myr, suggesting tidal migration may drive planets inward. These results provide one of the first observational demographic indicators that the radius distribution of small, short-period planets evolves with time, shaped by atmospheric escape and migration.