^Nyva Vinnytsia renamed themselves from Nyva-Svitanok prior to the start of the season
^FC Dnipro Cherkasy deducted 6 points by the Ukrainian Football Federation. Three points on November 2, 2008 and three points on March 26, 2009. The club failed to arrive for their 29th and 30th Round games and subsequently were expelled from the competition by the PFL.[6]
^FC Podillya-Khmelnytskyi renamed themselves to Dynamo Khmelnytskyi on March 2, 2009.[7]
^MFK Mykolaiv were readmitted into the PFL after dissolving at the end of the Persha Liha 2007–08 season at the expense of FC Dynamo-3 Kyiv who withdrew from the competition
^FC Korosten deducted 3 points by the Ukrainian Football Federation on March 26, 2009. After not arriving for their 22nd-round game against Veres Rivne, the PFL expelled FC Korosten from the professional leagues.[8]
^Prior to the start of the season FC Olimpik Kirovohrad changed back its name to Zirka, and Zirka that participated in amateur competitions became Olimpik.
^ abcFC Tytan Donetsk, FC Shakhtar Sverdlovsk, and FC Hirnyk Kryvyi Rih deducted three points on June 18, 2009.[9]
^ abcdFC Arsenal Kharkiv, FC Hirnyk Kryvyi Rih, FC Dnipro-75 Dnipropetrovsk, and FC Sumy were deducted three points for non-paying the participation fees; FC Hirnyk Kryvyi Rih, FC Dnipro-75 Dnipropetrovsk, and FC Sumy were deducted additional three points for non-paying the participation fees for the second half of the season. The decision was officially declared by the Disciplinary Committee of PFL on May 28, 2009[10]
^FC Kremin Kremenchuk deducted 3 points by the Ukrainian Football Federation March 26, 2008
^FC Yavir Krasnopillya changed their name to FC Sumy on September 11, 2008
^С ФК "Харьков" сняли три очка [FC Kharkiv deducted three points)] (in Russian). UA Football. 2009-05-13. Archived from the original on 14 May 2009. Retrieved 2009-05-15.