The defender - National League Player of the Month for September - will likely sit out the rest of January.
It’s the latest defensive issue for Justin Edinburgh after Josh Coulson, 29, was also ruled out for “several weeks” with a hamstring injury.
However George Elokobi is back in action after missing most of the season.
“The club can confirm defender Marvin Ekpiteta has suffered an upper ankle sprain and is expected to miss a few weeks of action,” read a club statement.
“The 23-year-old has made 28 National League appearances this campaign, scoring four goals, before picking up the injury in Saturday's FA Trophy victory over Wrexham.
“We wish him a quick recovery and look forward to seeing him return to action as soon as possible.”