The knock-out tournament was broadcast on Fox Footy on Tuesday nights.
Despite a $100,000 prize, the format struggled to get support from some clubs as they preferred to focus on their main competition.
Foxtel, a broadcast partner of the AFL, is likely to put more resources into its highly successful reality show The Recruit, with a second season planned for next year.
"The Foxtel Cup has been a very strong competition for our state leagues over the last four seasons," a League spokesman told AFL.com.au.
"As our state leagues continue their development, we are discussing with the various state associations how best they wish to structure their competition requirements, including whether this competition will continue," he said.
"We expect a final decision to be reached in the near future."
It's understood one possibility could be an annual, one-off match between the WAFL and SANFL premiers, which could be broadcast locally in both states.