This study was carried out to compare the effects of flushing diets with different levels of extruded flaxseed (EFS) and rumen undegradable protein (RUP) on reproductive performance and blood metabolites in Baluchi ewes. Forty-eight ewes (2–3 years old) were fed one of four different treatment diets: 1) no EFS + 20% RUP, 2) no EFS + 40% RUP, 3) 10% EFS + 20% RUP and 4) 10% EFS + 40% RUP. Blood concentrations of glucose (24 h after removing controlled internal drug release (CIDR) containing 0.3 g of progesterone) and cholesterol (24 h before removing CIDR) were different among the dietary treatments (P < 0.05). Blood urea-N (24 h after removing CIDR and 9 days after mating) was also impacted by the dietary treatments (P < 0.05). Higher blood estrogen levels occurred in response to EFS supplementation plus 40% RUP in comparison to non-EFS diets both 24 h before and after removing CIDR. Blood progesterone in ewes fed 10% EFS and 40% RUP diet was increased 9 days after mating in comparison to ewes fed non-EFS diets (P < 0.05). 10% EFS and 40% RUP in the diets of ewes improved the fecundity rate (P < 0.05). Follicle and corpus diameter (24 h after CIDR removal and 9 days after mating, respectively) were higher in EFS diets than the other groups (P < 0.05). So, the use of 10% EFS as a source of omega-3 fatty acids with 40% RUP in the flushing diet can improve ewe reproduction performance, which is important in the sheep industry, especially in developing countries.