The exchange will be offered only during the weekend of July 6-7 at the Patriots Pro Shop.
Earlier this week, Hernandez was charged in the murder of an acquaintance and released by the Patriots.
"We know that children love wearing their Patriots jerseys but may not understand why parents don't want them wearing their Hernandez jerseys anymore," Patriots spokesman Stacey James said in a statement. "We hope this opportunity to exchange those jerseys at the Patriots Pro Shop for another player's jersey will be well received by parents."
The pro shop will be open from 10 a.m.-9 p.m. July 6 and from 10 a.m.-7 p.m. July 7.