The office of the Accountant General, Arunachal Pradesh, has a history dating back to 1910 when the Office of the Comptroller, Assam, was established at Shillong. That office gained the status of an Accountant General’s Office in 1952, and functioned as a composite Audit & Accounts Office of the then undivided State of Assam. With the creation of the States of Nagaland, Tripura and Manipur and setting up of Accountants General Offices in the State Capitals of these three States in 1973, the geographical jurisdiction of the Office of the Accountant General at Shillong, was reduced.

In March 1984, the Indian Audit & Accounts Department was bifurcated into the Audit Wing and the Accounts & Entitlements (A&E) Wing, and four Accountants General Offices, all with Headquarters at Shillong, were created - Offices of the (i) Principal Accountant General (Audit), Assam; (ii) Accountant General (A&E), Assam; (iii) Principal Accountant General (Audit); Meghalaya, Arunachal Pradesh & Mizoram; and (iv) Accountant General (A&E), Meghalaya, Arunachal Pradesh & Mizoram

In course of time, the offices of the Accountants General, Assam, shifted from Shillong to Guwahati. With the creation of new Accountants General Offices for Mizoram in Aizawl and Arunachal Pradesh in Itanagar in April 2006, the two Accountants General Offices at Shillong were re-designated as Offices of the Principal Accountant General (Audit), Meghalaya, and Accountant General, (A&E), Meghalaya

The Accountants General function under the powers vested in the Comptroller & Auditor General of India by the Constitution of India and the Comptroller & Auditor General's {Duties, Powers & Conditions of Services (DPC)} Act, 1971.

The Accountant General, Arunachal Pradesh, is also responsible for compiling and preparing the Annual Accounts (Finance Accounts & Appropriation Accounts) of the Government of Arunachal Pradesh and to submit the Accounts to the Governor for placing it before the State Legislature in accordance with Articles 149 and 151 of the Constitution of India, read with Section 11 of the Comptroller & Auditor General of India (DPC) Act, 1971.