The building, located on North Greensboro Street, was recently purchased by CVS from the local co-op grocery store, Weaver Street Market.
The fence is in response to the Feb. 5 occupation of a vacant building that now sits on site.
At the occupation, masked protesters, some who identify as anarchists and are loosely linked to the Occupy Chapel Hill movement, took over the building in an attempt to convert it into a community center.
Mayor Mark Chilton met with the protesters and personally asked them to leave before having the police step in and threaten arrest.
On Wednesday, dozens of people showed up to a meeting with developers at Carrboro Town Hall to hear more about a plan to turn the building into a two-story CVS drug store.
At that meeting, developer Leigh Polzella mentioned the idea of a fence and said, "In light of this weekend's events, we are re-securing the property ASAP."
CVS wants zoning laws changed, so it can build the new store. Currently, CVS has a store a short distance down North Greensboro Street next to the Harris Teeter.
Because of this, some residents feel there could be better uses for the building, and at the meeting, some suggestions called for a library.
Residents also spoke about traffic concerns, and the potential environmental effects of construction.
A zoning meeting on the project is set for early next month.