Josephson junctions have broad applications in metrology, quantum information processing, and remote sensing. For these applications, the electronic noise is a limiting factor. In this work we study the thermal noise in narrow Josephson junctions using a tight-binding Hamiltonian. For a junction longer than the superconducting coherence length, several self-consistent gap profiles appear close to a phase difference pi. They correspond to two stable solutions with an approximately constant phase gradient over the thin superconductor connected by a 2 pi phase slip, and a solitonic branch. The current noise power spectrum has pronounced peaks at the transition frequencies between the different states in each branch. We find that the noise is reduced in the gradient branches in comparison to the zero-length junction limit. In contrast, the solitonic branch exhibits an enhanced noise and a reduced current due to the pinning of the lowest excitation energy to close to zero energy.