Innovative management practices are needed to mitigate greenhouse gas (GHG) emissions from the agricultural sector by enhancing soil carbon (C) and nitrogen (N) stocks, which serve as major reservoirs of C and N in the terrestrial ecosystem. The effect of cropping systems and N fertilization rates were examined on soil organic C (SOC) and soil total N (STN) stocks at the 0–120 cm depth from 2011 to 2018 in a dryland farm in the US northern Great Plains. Cropping systems were no-till continuous spring wheat (Triticum aestivum L.) (NTCW), no-till spring wheat–pea (Pisum sativum L.) (NTWP), no-till spring wheat–fallow (NTWF), and conventional till spring wheat–fallow (CTWF) and N fertilization rates were 0, 50, 100, and 150 kg N ha−1 applied to spring wheat. The SOC and STN were greater for NTWP than other cropping systems at most N fertilization rates and depth layers. Increasing N fertilization rate increased SOC at 0–30 cm for NTWP and NTCW, but had a variable effect on STN for various cropping systems and soil depths. The NTWP with 50–100 kg N ha−1 can enhance SOC and STN at 0–30 cm compared to other cropping systems and N fertilization rates in the US northern Great Plains.