| Flag | Date | Use | Description |
| 2012–present | Aerodrom Municipality | |
| ? – Present | Aračinovo Municipality | A red flag with the coat of arms in the middle and two thin horizontal stripes. |
| ? – Present | Berovo Municipality | A light blue flag with red insignia in the middle. |
| 2006–present | Bitola Municipality | A white background with the municipal coat of arms, in the middle. |
| ? – Present | Bogdanci Municipality | A blue and red flag, with the Municipality coat-of-arms in the middle. |
| 1996–present | Bogovinje Municipality | A red background with the municipal coat of arms, in the middle. |
| 1996–present | Bosilovo Municipality | |
| | Brvenica Municipality | |
| 2010–present | Čair Municipality | A white background with the municipal coat of arms, in the middle. |
| | Čaška Municipality | |
| ?–2014 | Municipality of Češinovo-Obleševo | |
| | Centar Župa Municipality | |
| | Municipality of Čučer-Sandevo | A white background with the municipal coat of arms, in the middle. |
| | Debar Municipality | |
| | Debarca Municipality | |
| | Municipality of Delčevo | |
| ?–2015 | Demir Hisar Municipality | |
| | Demir Kapija Municipality | A yellow background with the municipal coat of arms, in the middle. |
| | Dojran Municipality | |
| | Dolneni Municipality | |
| ?-Present | Gevgelija Municipality | A flag with a blue bar over a white bar & the coat-of-arms of the Municipality near the mast of the flag. |
| | Gostivar Municipality | |
| 1996–present | Ilinden Municipality | A red vertical flag with a 12-pointed sun and the letter "I" in Cyrillic. |
| | Jegunovce Municipality | |
| | Karbinci Municipality | A white background with the municipal coat of arms, in the middle. |
| | Kavadarci Municipality | |
| ?–2015 | Kisela Voda Municipality | |
| 2010–present | Municipality of Kočani | |
| | Konče Municipality | A red background with the municipal coat of arms, in the middle. |
| 2006–present | Kratovo Municipality | |
| 2009–present | Kriva Palanka Municipality | |
| 2005–present | Karpoš Municipality | A yellow background with the municipal coat of arms, in the middle. |
| | Municipality of Krivogaštani | A red background with the municipal coat of arms, in the middle. |
| | Municipality of Kruševo | |
| 2002–Present | Kumanovo Municipality | A red background with the municipal coat of arms, in the middle. |
| | Lipkovo Municipality | |
| | Lozovo Municipality | |
| ?-Present | Makedonska Kamenica Municipality | |
| | Makedonski Brod Municipality | |
| | Municipality of Mavrovo and Rostuša | |
| | Mogila Municipality | |
| | Negotino Municipality | |
| | Novaci Municipality | |
| | Novo Selo Municipality | |
| | Municipality of Pehčevo | |
| | Petrovec Municipality | |
| | Plasnica Municipality | - |
| ? – Present | Prilep Municipality | A dark blue background with the municipal coat of arms, outlined in white, in the middle. |
| 2015–present | Municipality of Probištip | |
| 2007–present | Rankovce Municipality | |
| | Resen (municipality) | A white background with the municipal coat of arms, in the middle. |
| | Rosoman Municipality | |
| | Skopje Municipality | |
| | Municipality of Sopište | |
| | Municipality of Staro Nagoričane | |
| | Municipality of Štip | A white background with the municipal coat of arms, in the middle. |
| ?-Present | Struga Municipality | A blue vertical flag with the coat of arms in the middle. |
| ?-Present | Strumica Municipality | A white vertical flag with the coat of arms and a blue-yellow border. |
| | Municipality of Studeničani | |
| ?-Present | Radoviš Municipality | |
| 2007–present | Tearce Municipality | |
| ?-Present | Tetovo Municipality | A red, black and yellow tricolor flag, the yellow one being the thickest. |
| | Valandovo Municipality | |
| | Vasilevo Municipality | |
| ?-Present | Veles Municipality | |
| ?-Present | Vevchani Municipality | |
| 2007–present | Vinica Municipality | A red and blue bicolor flag with outline of Vinica Fortress and an icon. |
| | Municipality of Vrapčište | |
| | Zelenikovo Municipality | |
| 1996–present | Municipality of Želino | |
| | Zrnovci Municipality | |
| | Šuto Orizari Municipality | A white background with the municipal coat of arms, in the middle. |