Agroforestry systems (AFS) have the potential to foster long-term carbon sequestration and nutrient uptake. Yet, information on sequestration rates is still scarce, especially for AFS in temperate regions and for maturing AFS. This study aims to determine the rate and amount of carbon and nitrogen uptake in a 17-year-old northern red oak (Quercus rubra)–pecan (Carya illinoinensis) silvopastoral planting in Fayetteville, AR, USA. Seven oak and pecan trees were felled to develop AFS-specific allometric equations for above-ground biomass, carbon, and nitrogen. Tree-stand woody biomass (DWw), carbon (Cw) and nitrogen (Nw) and leaf biomass (DWL), carbon (CL), and nitrogen (NL) were calculated with these equations. Diameter at 1.37 m above ground (DBH) was measured annually, and a non-linear mixed-effect model was used to estimate absolute (AGR) and relative growth rates. DWw and Cw was 7.1 and 3.4 Mg ha−1 for pecan and 26.6 and 12.7 Mg ha−1 for oak, which corresponds to a carbon sequestration rate of 0.75 and 0.20 Mg C ha−1 yr−1, respectively. Total N uptake was approximately 66 and 71 g N tree−1 yr−1 for oak and pecan. The mixed-effect model with individual-tree-level random effects for all parameters provided the best representation of DBH growth of oak and pecan, likely due to the high heterogeneity of site characteristics. The AGR explained the non-linear plant growth and reached its maximum of 0.017 and 0.0179 m yr−1 for oak and pecan, respectively, 11 years after planting. This suggests that carbon and nitrogen uptake also declined after 11 years.