At the end of the 2010 season, two new clubs, Kamatamare Sanuki and Nagano Parceiro, were promoted from the Japanese Regional Leagues by virtue of their final placing in the Regional League promotion series. Kamatamare Sanuki were approved as J. League associate members at the annual meeting in February. Applications by Zweigen Kanazawa and FC Ryukyu were given "continuous deliberations" status with further efforts required to obtain the membership. The earthquake and tsunami led to significant changes in competition schedule. Besides the postponement of the tournament, Sony Sendai, who were the most affected by disaster and couldn't recover in time, asked the league to put them on temporary hiatus. Missing the first eleven rounds (7th to 17th), Sony re-joined the league on 3 July and continued participation from then on. The final tournament schedule is as follows: Every team in the league will play 33 games: Two against each other (home and away) and one against Sony Sendai according to the schedule of the second half of the tournament (rounds 18th to 34th). Sony Sendai will play 17 games against every other team in the second half of the tournament. Sony Sendai will also participate in the rescheduled games of rounds 1–6, called "Matches for reconstruction assistance of Tōhoku earthquake and tsunami" (東日本大震災 災害復興支援試合). Although those games are treated as official JFL matches, they will not be included into the league results. For the purpose of determining the relegated teams, Sony Sendai can add points gained in six aforementioned "reconstruction" games to their official 17-match outcome. Thus, Sony Sendai will be judged by 23 matches, while every other team – by 33. On 3 August JEF Reserves had submitted a request of withdrawal from the league at the end of the season due to difficult financial conditions and poor performances of the team. The request was approved by the league Board on 12 September. In the penultimate round Sagawa Shiga won their third JFL championship in only five years of existence, firmly placing themselves among the strongest amateur teams in Japan. Two clubs, Machida Zelvia and Matsumoto Yamaga were promoted to J. League. By virtue of their placing in the Regional League promotion series, three clubs were promoted to JFL at the end of the season: YSCC Yokohama, Fujieda MYFC, and Hoyo AC Elan Oita. Because of JEF Reserves' withdrawal, no additional promotion and relegation play-offs were held.

Updated to games played on 11 December 2011. Source: Japan Football League Rules for classification: 1) points; 2) goal difference; 3) number of goals scored† FC Ryukyu and Honda Lock occupied top 2 places at the end of the 17th round (11th week) and were seeded for 2011 Emperor's Cup. These clubs were automatically qualified for the tournament, while each of other JFL clubs had to go through the prefectural qualifier.1 Must hold J. League Associate Membership, pass a final inspection by J. League (club name shown in bold) and finish no less than in fourth place to be promoted. V-Varen Nagasaki, though being an associate members, have announced that their stadium is not matching the J. League standards so they are not eligible for the promotion until the completion of necessary renovations. The target date is set for 2013 season. Because the maximum capacity of Division 2 set by J. League is 22 teams, no more than two clubs can be promoted.2 Arte Takasaki decided to withdraw from JFL and fold the club after the end of the season, when clubs promoted from regional leagues were already determined. JFL decided that the next season will be contested by 17 clubs (i.e. without supplying an additional club from a regional league).3 JEF Reserves had submitted a request of withdrawal from the league at the end of the season regardless of team's performance. It was approved by league board on 12 September.(C) = Champion; (R) = Relegated; (P) = Promoted; (E) = Eliminated; (O) = Play-off winner; (A) = Advances to a further round. Only applicable when the season is not finished:(Q) = Qualified to the phase of tournament indicated; (TQ) = Qualified to tournament, but not yet to the particular phase indicated; (RQ) = Qualified to the relegation tournament indicated; (DQ) = Disqualified from tournament.

Updated to games played on 11 December 2011. Source: Japan Football League: First round, second round 1 ^ The home team is listed in the left-hand column.2The postponed Sony Sendai matches from rounds 1–6, called "Matches for reconstruction assistance of 2011 Tōhoku earthquake and tsunami" (東日本大震災 災害復興支援試合). Those games are treated as official JFL matches but are not included into the final results.3The game was originally scheduled to 7 August, but was abandoned after the first half (0–0) because of the heavy thunderstorm. The remaining 45 minutes were played on 19 October. [1]Colours: Blue = home team win; Yellow = draw; Red = away team win. For coming matches, an a indicates there is an article about the match.

Updated to games played on 11 December 2011 Source: Japan Football League: First round, second roundNotes:† Team played previous season in Regional Leagues.