In this paper, we prove a general existence theorem for properly embedded minimal surfaces with free boundary in any compact Riemannian 3‐manifold M with boundary ∂M. These minimal surfaces are either disjoint from ∂M or meet ∂M orthogonally. The main feature of our result is that there is no assumptions on the curvature of M or convexity of ∂M. We prove the boundary regularity of the minimal surfaces at their free boundaries. Furthermore, we define a topological invariant, the filling genus, for compact 3‐manifolds with boundary and show that we can bound the genus of the minimal surface constructed above in terms of the filling genus of the ambient manifold M. Our proof employs a variant of the min‐max construction used by Colding and De Lellis on closed embedded minimal surfaces, which were first developed by Almgren and Pitts.