The league announced on April 6, 2012, that the expansion franchise Chicago Express had withdrawn from the ECHL, effective immediately. The Express finished their inaugural season ninth in the Eastern Conference with a record of 34 wins, 26 losses, 8 overtime losses, and 4 losses in shootouts, eliminating them from playoff contention. The team also finished last in the league for attendance, averaging 2,508 fans per game (compared to the league average of 4,282 fans per game).
The league's annual Board of Governors meeting concluded on June 25, 2012. Announcements included the re-election of Steve Chapman, president of the Gwinnett Gladiators, to his seventh term as board president, capping of league membership at 26 teams, adoption of a two-referee system for the conference finals and Kelly Cup finals, and the league re-alignment for the 2012–13 season. The San Francisco Bulls joined the Western Conference's Pacific Division, while in the Eastern Conference, the Orlando Solar Bears joined the South Division and the Fort Wayne Komets and Evansville IceMen joined the North Division following the departure of the Chicago Express. The league also voted to table any decision regarding the playoff format until the Board of Governors' preseason meeting.
The preseason Board of Governors meeting was held on September 27, 2012. Announcements included changes to the Kelly Cup playoff format and a change to the league's reserve list policy. The 3-day and 7-day injured reserve spots were changed to two generic reserve spots with no minimum stay required. No change was made to the 21-day reserve list policy.
The 2013 Kelly Cup playoffs format represented a significant departure from previous years. Eight teams qualified in the Eastern Conference: the three division winners plus the next five teams in the conference. With the addition of the expansion franchise in San Francisco, the Board of Governors changed the Western Conference seeding such that eight teams qualified: two division winners and the next six teams in the conference. This eliminated the Western Conference first-round bye. 
Similar to the NHL, the division winners were seeded as the top three seeds in the Eastern Conference and the top two seeds in the Western Conference; the conference winner faces the eighth seed, second faces seventh, third faces sixth and fourth faces fifth in the conference quarterfinal round. The winner of the 1st/8th series plays the winner of the 4th/5th series while 2nd/7th winner plays against the 3rd/6th winner in the conference semifinal series.
The Board of Governors also elected to change the playoff format such that all rounds of the playoffs are now best of seven series. For 2012-13, the Conference Finals and Kelly Cup Finals will use a two-referee system.