Warm periods in Earth’s history offer opportunities to understand the dynamics of the Earth system under conditions that are similar to those expected in the near future. The Middle Pliocene warm period (MPWP), from 3.3 to 3.0 My B.P, is the most recent time when atmospheric CO2 levels were as high as today. However, climate model simulations of the Pliocene underestimate high-latitude warming that has been reconstructed from fossil pollen samples and other geological archives. One possible reason for this is that enhanced non-CO2 trace gas radiative forcing during the Pliocene, including from methane (CH4), has not been included in modeling. We use a suite of terrestrial biogeochemistry models forced with MPWP climate model simulations from four different climate models to produce a comprehensive reconstruction of the MPWP CH4 cycle, including uncertainty. We simulate an atmospheric CH4 mixing ratio of 1,000 to 1,200 ppbv, which in combination with estimates of radiative forcing from N2O and O3, contributes a non-CO2 radiative forcing of 0.9 W⋅m−2 (range 0.6 to 1.1), which is 43% (range 36 to 56%) of the CO2 radiative forcing used in MPWP climate simulations. This additional forcing would cause a global surface temperature increase of 0.6 to 1.0 °C, with amplified changes at high latitudes, improving agreement with geological evidence of Middle Pliocene climate. We conclude that natural trace gas feedbacks are critical for interpreting climate warmth during the Pliocene and potentially many other warm phases of the Cenezoic. These results also imply that using Pliocene CO2 and temperature reconstructions alone may lead to overestimates of the fast or Charney climate sensitivity.