© 2018 The Author(s). Published by IOP Publishing Ltd. In the last few decades, temperatures in the Arctic have increased twice as much as the rest of the globe. As permafrost thaws in response to this warming, large amounts of soil organic matter may become vulnerable to decomposition. Microbial decomposition will release carbon (C) from permafrost soils, however, warmer conditions could also lead to enhanced plant growth and C uptake. Field and modeling studies show high uncertainty in soil and plant responses to climate change but there have been few studies that reconcile field and model data to understand differences and reduce uncertainty. Here, we evaluate gross primary productivity (GPP), ecosystem respiration (Reco), and net ecosystem C exchange (NEE) from eight years of experimental soil warming in moist acidic tundra against equivalent fluxes from the Community Land Model during simulations parameterized to reflect the field conditions associated with this manipulative field experiment. Over the eight-year experimental period, soil temperatures and thaw depths increased with warming in field observations and model simulations. However, the field and model results do not agree on warming effects on water table depth; warming created wetter soils in the field and drier soils in the models. In the field, initial increases in growing season GPP, Reco, and NEE to experimentally-induced permafrost thaw created a higher C sink capacity in the first years followed by a stronger C source in years six through eight. In contrast, both models predicted linear increases in GPP, Reco, and NEE with warming. The divergence of model results from field experiments reveals the role subsidence, hydrology, and nutrient cycling play in influencing the C flux responses to permafrost thaw, a complexity that the models are not structurally able to predict, and highlight challenges associated with projecting C cycle dynamics across the Arctic.