The following agreements have been concluded between Estonia and North Macedonia:

• Agreement on International Road Transport of Passengers and Goods between the Republic of Estonia and the Republic of Macedonia, signed 30.05.2000 (came info effect 22 August 2000)
• Agreement on the Avoidance of Double Taxation and Prevention of Tax Evasion (signed 20 November 2008, came into effect 21 May 2009)
• Agreement on the Exchange and Mutual Protection of Classified Information (signed 20 November 2008, came into effect 1 June 2009)
• Implementation Protocol between the Government of the Republic of Estonia and the Government of the Republic of Macedonia on the Readmission on Illegally Residing Individuals Agreement between the European Community and the Former Yugoslav Republic of Macedonia (signed 23 April 2010, came into effect 23 July 2010)

 Look for more detailed data about export and import from the application of the Statistics Estonia.

Defence co-operation between Estonia and North Macedonia began in 2004. Many soldiers of North Macedonia have studied in Estonia and from 2004-2007, Estonia sponsored the studies of three soldiers of North Macedonia at the Baltic Defence College. During the 2007-2008 academic year, a representative of North Macedonia took part in the Joint Command and General Staff Course and in 2009 in the Army Intermediate Command and Staff Course.

• Estonia took part in the EU’s military mission Concordia from 31.03.2003 – 15.12.2003 with one staff officer.
• Estonia took part in the EU Police Mission Proxima from 15.12.2003 - 14.12.2005 with 1 staff officer.

Over the years Estonia has supported North Macedonia in implementing many projects. These have primarily been aimed towards developing Macedonian e-government. Some projects that have taken place over the years:

• From 11-16.05.2008, the e-Governance Academy organised a training course in Tallinn for state officials of North Macedonia on the usage of information technology and the division of labour among the Estonian Land Board and the other establishments in its jurisdiction.
• From 2-3.06.2008 an expert of the Estonian Land Board consulted officials of North Macedonia on-site.
• From 19.-22.10.2008 a representative of AS Cybernetica visited North Macedonia and consulted with IT Minister Ivo Ivanovski on X-Road matters.
• From May-October 2010 a project was carried out in North Macedonia in order to share Estonia’s experiences with establishing an electronic identity system.
• Estonia has provided scholarships for diplomats from North Macedonia to attend the Estonian School of Diplomacy. Most recently a Macedonian student attended the school during the 2013/2014 academic year.
• In April 2012 a group from North Macedonia came to Estonia for a study trip, which was funded by resources from the European Union TAIEX programme. During the trip, Estonia shared its experiences with implementing international sanctions.
• During 2014-2015, in the framework of development cooperation, Estonia supported a project to develop the telephone based medical counselling for the inhabitants of North Macedonia.
• In October 2014 a study visit of three journalists from North Macedonia to Baltic Film, Media, Arts and Communication School took place, financed by the Estonian development cooperation budget.
• In March 2015 a Macedonian business delegation visited Tallinn and participated in a business forum in the Estonian Chamber of Commerce and Industry, which was also financed by the Estonian development cooperation budget.
• In September and October 2015 the Ministry of Social Affairs and the Personnel Manager from the Ministry of Finance carried out a TAIEX project for civil servants of North Macedonia about the labour market and work related legislation.
• Estonian Agricultural Registers and Information Board participates in North Macedonia together with the Netherlands and Slovenia in a Twinning project in the area of agriculture and agricultural registers. The aim of the project is to further strengthen the AFSARD (Agency for Financial Support of Agriculture and Rural Development of North Macedonia) and to help the Agency to prepare for the EU aid programming period 2014-2020.
• In May 2016 a TAIEX Study Visit on the Use of Digital Certificates for Public Services  took place in Tallinn. 
• On March 30, 2016 the Estonian Auditors' Association signed a memorandum of cooperation with the Council for Advancement and Oversight of Audit of the Republic of North Macedonia (CAOARM) in Tallinn. The cooperation will involve staff of both institutions through exchange of information, know-how and skills, thus enhancing the institutional capacities.
• In 2016 an Estonian expert carried out training on statistics for health sector officials of North Macedonia, financed by WHO.
• An Estonian NGO "Eesti Abikeskused" implemented from January 2016 to March 2017 a project in North Macedonia which was funded by the IPA programme „Increasing the supply of the qualified work-force among the labour market risk-groups in Macedonia".
• In June 2019 the Ministry of Foreign Affairs organised a study visit for a group of journalists from Western Balkan countries to Tallinn (two journalists from North Macedonia participated in the visit).