We construct supersymmetric AdS 3 solutions in F-theory, that is Type IIB supergravity with varying axio-dilaton, which are holographically dual to 2d N = (0, 4) superconformal field theories with small superconformal algebra. In F-theory these arise from D3-branes wrapped on curves in the base of an elliptically fibered Calabi-Yau threefold Y 3 and correspond to self-dual strings in the 6d N = (1, 0) theory obtained from F-theory on Y 3 . The non-trivial fibration over the wrapped curves implies a varying coupling of the N = 4 Super-Yang-Mills theory on the D3-branes. We compute the holographic central charges and show that these agree with the field theory and with the anomalies of self-dual strings in 6d. We complement our analysis with a discussion of the dual M-theory solutions and a comparison of the central charges.