Prime Minister Khorloogiin Choibalsan arranged for his arrest and subsequent execution on charges of counterrevolution in 1940 to free up the party leadership role for Yumjaagiin Tsedenbal.

In October 1936 he was elected member of the Presidium and General Secretary of the Central Committee of the MRPR.

[1] In December 1939 Choibalsan and then Deputy Minister of Finance Tsedenbal traveled to Moscow to meet with Josef Stalin.

Stalin made known his wishes to see the 23-year-old Tsedenbal, whom the Soviet leadership had earlier handpicked for advancement, promoted to Secretary General of the MPRP.

Upon his return, Choibalsan orchestrated Baasanjav's arrest and subsequent execution on charges of counterrevolution in February 1940.