The first systematic study of the BaO–B2O3 system and barium orthoborate Ba3B2O6 (3BaO·B2O3) was reported in 1949. Thereafter, the system was repeatedly refined but the structure of Ba3B2O6 compound has not been adequately studied yet. In our study we have, for the first time, obtained the crystalline samples of Ba3B2O6. The solved structure (Pbam, a = 13.5923(4) Å, b = 13.6702(4) Å, c = 14.8894(3) Å) belongs to the class of ‘anti-zeolite’ borates with a pseudotetragonal [Ba12(BO3)6]6+ cation pattern which contains channels along the c axis filled with anionic clusters. The Ba3B2O6 compound may be regarded as a fluorine-free end-member of the Ba3(BO3)2– xF3x solid solution. The BaO–B2O3 phase diagram presented in our study is based on our research and literature data.