In this paper we calculate the Casimir energy for a massless fermionic field confined inside a three-dimensional rectangular box. We use the MIT bag model boundary condition for the confinement. We use the direct mode summation method along with the Abel-Plana summation formula to compute the Casimir energy, without any use of regularization or analytic continuation techniques.We obtain a negative Casimir energy, as opposed to the previously reported result for the interior of a three-dimensional sphere.