The Missaukee Branch complex included a number of branch lines that stemmed from the main part of the branch, itself branching from the PRR mainline at Misaukee Junction and heading east to Lake City and ultimately to Falmouth, MI. Other branches include:
- Jennings Branch: This line branched from the Missaukee Branch at Round Rock Junction and headed north to the town of Jennings, MI.
- Lake City Branch: This short branch joined the Missuakee Branch at Lake City Junction (at Sandstown) and a little over a mile north to Lake City.
Each of these branches were abandoned at various times, and the last vestige of this branch complex included the main part of the branch between Missaukee Junction and Lake City. In its later years, the line was operated by the Cadillac and Lake City Railway, from 1964 to 1971. This remaining section was finally abandoned in 1984.