Poor soil fertility is a major constraint to crop productivity in the highlands of Ethiopia. This study was conducted to evaluate the effects of nitrogen (N) fertilization, variety and growing season on grain yield and yield related traits, and determine relationships among agronomic traits of malting barley. The treatments studied were five N levels (0, 23, 46, 69 and 92 kg ha−1) and two malting barley varieties (Miscal-21 and Holker) over three growing seasons (2012, 2013 and 2014) at Bekoji, south eastern Ethiopia. The results revealed that as N rates increased, grain yield, number of tillers and spikes per square meter, biomass yield at harvest, days to physiological maturity, spike length and number of kernels per spike increased, but harvest index decreased. Grain yield, harvest index, number of tillers and spikes per square meter, spike length and biomass yield at harvest were greater in Miscal-21, whilst days to maturity and number of kernels per spike were greater in Holker. Grain yield, harvest index, number of tillers and spikes per square meter, spike length, biomass yield at harvest and days to maturity were significantly affected by seasonal conditions, but spike length and kernels per spike were not affected. Grain yield was positively influenced by the number of tillers per square meter, biomass yield at harvest, spikes per square meter, spike length, kernels per spike and harvest index. However, the number of tillers per square meter followed by biomass yield and spikes per square meter largely determined grain yield. The results of the current study suggest that genetic improvement of those yield related traits is the likely basis of increasing grain yield in barley.