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We investigate the combined effects of a magnetic flux-carrying cosmic string and a brane on the fermionic condensate (FC) and on the vacuum expectation value (VEV) of the energy-momentum tensor for a massive charged fermionic field in background of 5-dimensional anti-de Sitter (AdS) spacetime. The brane is parallel to the AdS boundary and it divides the space into two regions with distinct properties of the fermionic vacuum. For two types of boundary conditions on the field operator and for the fields realizing two inequivalent representations of the Clifford algebra, the brane-induced contributions in VEVs are explicitly separated. The VEVs are even periodic functions of the magnetic flux, confined in the core, with the period of flux quantum. Near the horizon the FC and the vacuum energy-momentum tensor are dominated by the brane-free contribution, whereas the brane-induced part dominates in the region near the brane. Both the contributions vanish on the AdS boundary. At large distances from the cosmic string, the topological contributions in the VEVs, as functions of the proper distance, exhibit an inverse power-law decrease in the region between the brane and AdS horizon and an exponential decrease in the region between the brane and AdS boundary. We show that the FC and the vacuum energy density can be either positive or negative, depending on the distance from the brane. Applications are discussed in fermionic models invariant under the charge conjugation and parity transformation and also in $Z_{2}$% -symmetric braneworld models. By the limiting transition we derive the expressions of the FC and the vacuum energy-momentum tensor for a cosmic string on 5-dimensional Minkowski bulk in the presence of a boundary perpendicular to the string.