Balanced nutrition is imperative for efficient nutrient management and has a considerable role in enhancing crop yield. To study the effect of various nitrogen sources at various sulfur levels on maize–wheat yield and N/S uptake under different climatic conditions, field experiments were conducted at Agronomy Research Farm, The University of Agriculture Peshawar, and Research Station Buner during 2018–2019. Nitrogen was applied at 150 kg ha−1 for maize and 120 kg ha−1 for wheat from inorganic (urea) and organic farm yard manure (FYM) sources at ratios of 100:0, 75:25, 50:50, 25:75, and 0:100, and sulfur levels from elemental sulfur of 0, 20, 40, and 60 kg ha−1. The study was carried out with a randomized complete block design with two-factorial arrangement and three replicates. Results shows that maximum 1000-grain weight, grain yield, biological yield, nitrogen uptake, and sulfur uptake were recorded at 50% organic and 50% inorganic nitrogen application for maize and wheat at both locations. Results regarding sulfur levels, maximum 1000-grain weight, grain yield, biological yield, and nitrogen uptake were recorded in the treatment group receiving 20 kg S ha−1 in Peshawar, and 40 kg S ha−1 in Buner; however, sulfur uptake increases with increase sulfur levels. The interaction between nitrogen sources and sulfur levels was significant; maximum grain yield and uptake of nitrogen and sulfur were recorded in the treatment group receiving 150 kg N ha−1 for maize and 120 kg N ha−1 for wheat along with 20 kg S ha−1 for Peshawar and 40 kg S ha−1 for Buner. Hence, it is recommended that 150 kg N ha−1 for maize and 120 kg N ha−1 for wheat (50% inorganic and 50% organic) along with 20 kg S ha−1 for Peshawar and 40 kg S ha−1 for Buner as a source of elemental sulfur be used for optimum grain yield and N/S uptake.