- The National Paying Agency under the Ministry of Agriculture of the Republic of Lithuania (hereinafter – the Agency) was established on 11 November 1999. Upon the establishment, the Agency employed 12 people.
- SAPARD support management has been the main objective of the Agency since its establishment. The right to manage this support autonomously was granted by the European Commission on 26 November 2001. The first collection of applications started in December 2001, with the first grant agreement signed with Raupaičių Ūkis, an agricultural cooperative enterprise of Šiauliai district, in January 2002.
- Upon the accession of Lithuania into the European Union in 2004, the Agency entered a new and much more difficult stage of activity, namely the management of the European Union’s Common Agricultural Policy measures. It started managing support under the measures of the Rural Development Plan 2004–2006 and the Rural Development and Fisheries Priority of the Single Programming Document of Lithuania for 2004–2006. A Single Payment Scheme for direct subsidy payments to landowners has been applied since 2004.
- The financial period 2007–2013 started in 2007. It coincided with the start of the implementation of the new Lithuanian Rural Development Programme 2007–2013. EUR 2.28 billion of support has been allocated under this programme.
- The payment of support under the Rural Development Plan 2004–2006 was finished on 31 December 2008 and that under Priority 4 of the Single Programming Document of Lithuania for 2004–2006 was completed on 30 June 2009.
- On 5 May 2009, the Agency was issued a certificate of compliance of the Agency’s information security management system with ISO/IEC 27001:2005 requirements.
- The process of application of a Common Assessment Framework was initiated at the Agency in December 2009.
- A Quality Management System has been implemented in accordance with LST EN ISO 9001:2008 in 2010.
- In 2012 the Agency was granted the National Quality Prize in the category of big enterprises. The annual competition of the National Quality Prize is organized by the Ministry of Economy of the Republic of Lithuania and the Quality Council.
- In 2013 Agency nominated for the European Knowledge Award. European Knowledge prize values European Union institutions efforts to help their employees to improve and broaden their professional knowledge.
- Environmental Management System LST EN ISO 14001:2005 installed at the end of 2014.
- The financial period 2014-2020 started in 2014. EUR 4.63 billion of support has been allocated under this programme.
- The structure of the Agency consists of the Management, 10 departments, 3 independent units and 10 regional units.