Small grain cereals in lower latitude areas usually mature under terminal drought conditions that affect their agronomic performance. An experiment was conducted to compare agronomic traits, grain yield, and protein content under control and terminal drought conditions of 15 two-row and 10 six-row barley (Hordeum vulgare L.) genotypes. The experiment was set up at two locations for two growing seasons (2011, 2012) and two treatments. One treatment was terminal drought (D) simulated by the mechanical removal of all leaf blades 7 d after the heading of each genotype, and a control (C) treatment in which plants were left intact. On average, defoliation caused a greater reduction in grain yield and protein content of the six-row genotypes (37.6% and 12.3%, respectively) than the two-row genotypes (28.8% and 7.1%, respectively). On the other hand, test weight of six-row genotypes showed better tolerance to terminal drought. According to the multivariate function analysis, the genotypes of both types of barley with a high test weight, a longer uppermost internode, and a longer grain filling period had high protein content under terminal drought stress. In contrast to six-row genotypes, it is possible to breed two-row genotypes that not only have high grain yield but also high protein content under both optimal and drought stress conditions.