The Samagra Shikhsa Scheme is implemented as a Centrally Sponsored Scheme with effect from financial year 2018-19 through a single State Implementation Society (SIS) at the State /UT level. 

At the National level, there is a Governing Council headed by the Minister of Education and a Project Approval Board (PAB) headed by Secretary, Department of School Education and Literacy, Ministry of Education, Govt. of India. 

Every year, Samagra Shiksha UT Mission Authority, A & N Islands, with the approval of Executive Committe under the chairmanship of Chief Secretary, A & N Administration (Chairman, Executive Committee) submits Annual Work Plan & Budget before the PAB of MoE. After appraisal, the PAB approves budget for the UT.  Andaman & Nicobar Islands being UT without legislature received 100% funding from MoE.

The Cabinet approved continuation of Samagra Shiksha Scheme upto 31st March 2026 as Samagra Shiksha 2.0.

The Samagra Shiksha 3.0 is under the process of re-imagination and re-structuring and will be effective for another five years i.e. from 2026-27 to 2030-31.