6 months before Toju died in 1648, he founded 'the site of Toju Shoin' in his hometown Kokawa Village (now Takashima City, Shiga Prefecture) to get an educational foothold for the pupils.
1648年（慶安元年）藤樹が亡くなる半年前に郷里である小川村（現在の滋賀県高島市）に「藤樹書院跡」を開き、門人の教育拠点とした。