We compute the holographic entanglement entropy in the gravity with higher curvature terms dual to d=4 N=2 SCFTs in F-theory using the method proposed in arXiv:1011.5819. The log term of this entanglement entropy reproduces the A-type anomaly of the dual SCFTs in F- theory using the gravity dual with the higher derivative term, which, using the field redefinition, can be transformed to the Gauss-Bonnet term in the subleading order of a derivative expansion. Our analysis shows that the 1/N^2 correction for the central charges should be produced from the gravity including higher derivative terms up to curvature squared terms. To obtain consistent results, we discuss the holographic c-theorem.
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