Multiscale or multiphysics problems often involve coupling of partial differential equations posed on domains of different dimensionality. In this work, we consider a simplified model problem of a 3d‐1d coupling and the main objective is to construct algorithms that may utilize standard multilevel algorithms for the 3d domain, which has the dominating computational complexity. Preconditioning for a system of two elliptic problems posed, respectively, in a three‐dimensional domain and an embedded one dimensional curve and coupled by the trace constraint is discussed. Investigating numerically the properties of the well‐defined discrete trace operator, it is found that negative fractional Sobolev norms are suitable preconditioners for the Schur complement of the system. The norms are employed to construct a robust block diagonal preconditioner for the coupled problem.