Von 1999 bis 2001 war Noew erneut Verteidigungsminister als Nachfolger von Georgi Ananiew unter Ministerpräsident Iwan Kostow. Während dieser Amtszeit half Bulgarien den östlichen Nachbarn Nordmazedonien die innere Ordnung im Land während des Ethnischen Konfliktes mit den Albanern wieder herzustellen und Noew war maßgeblich an der Militärhilfe Bulgariens für die Streitkräfte von Nordmazedonien beteiligt.[5][6] Sein Nachfolger im Amt wurde Nikolaj Swinarow.
↑Inter-Parliamentary Conference for the Common Foreign and Security Policy (CFSP) and the Common Security and Defence Policy (CSDP). In: Bulgarische EU-Ratspräsidentschaft. Abgerufen am 9. Januar 2022 (englisch): „Boyko Noev. Minister of Defense of the Republic of Bulgaria (1994–1995 and 1999–2001) and Ambassator to NATO (1996–1999)
Ambassador Boyko Noev has served as Deputy Minister of Defense (1994) and Minister of Defense (1994–1995 and 1999–2001). With an educational background in International Relations and years of experience as a diplomat on the international stage he was the Bulgarian Ambassador to NATO, Belgium and Luxembourg (1996–1999). During his diplomatic career at the Bulgarian Ministry of Foreign Affairs (1981–1999), Ambassador Noev was also member and deputy-head of the Bulgarian delegations to the OSCE and the Treaty on Conventional Armed Forces in Europe. He served as Director, Center for National Security Studies at the Ministry of Defense (1993). He is the author of many publications and media appearances and has affiliations with the NGO sector and consultancy entities.“