Baryon inhomogeneitites formed in the early universe are important as they affect the nucleosynthesis calculations. Since they are formed much before the nucleosynthesis epoch, neutrino inflation plays a crucial role in damping out these fluctuations. Now neutrinos, in turn, are affected by magnetic fields which may be present in the early universe. In this work we study the evolution of baryonic inhomogeneities due to neutrino induced dissipative processes in the presence of a background magnetic field. We find that at higher temperatures the dissipation of the inhomogeneities are enhanced as the magnetic field increases. Our study also shows that at lower temperatures the same magnetic field may produce less dissipation. Though we limit our study to temperatures below the quark-hadron transition we do establish that magnetic fields present in the early universe affect the dissipation of baryonic inhomogeneities.