Hyperthermals—episodes of abrupt global warming associated with the massive injection of carbon into the oceans and atmosphere—represent possible analogs for future climate change. However, uncertainties in their magnitude, rate, and duration arising as a result of mixing processes and changes in carbonate preservation as the sediment record is formed complicate their use in constraining climate sensitivity and the role of carbon cycle feedbacks. Here, we use cGENIE, an Earth system model of intermediate complexity, to assess likely magnitude and rate of carbon input, taking a small hyperthermal event from the early-middle Eocene, C22nH3 (~49.2 Ma) as a case study. We develop an iterative method combined with a sediment model simulating the formation and mixing of deep-sea sediments to converge on an estimate for the “true” magnitude of the carbon cycle perturbation in the atmosphere and ocean that drives the event. In inverting the −0.95‰ benthic δ13C excursion recorded at Ocean Drilling Program Site 1258, we obtain an estimate of at least −1.45‰ for the atmospheric CO2 δ13C excursion that drove event C22nH3. We also assess controls on intersite variation of event shape in model sediments and find that sedimentation rate is the strongest determinant of modeled event size, with higher sedimentation rate sites recording the atmospheric signal more accurately. Our revised estimate for the size of C22nH3 implies a total carbon input almost two-thirds higher than would be deduced if the recorded δ13C excursion magnitude was taken at face value.