We consider a large neutral molecule with total nuclear charge Z in a model with self-generated classical magnetic field and where the kinetic energy of the electrons is treated relativistically. To ensure stability, we assume that Za < 2/p, where a denotes the fine structure constant. We are interested in the ground state energy in the simultaneous limit Z ¿ 8, a ¿ 0 such that ¿ = Za is fixed. The leading term in the energy asymptotics is independent of ¿, it is given by the Thomas-Fermi energy of order Z7/3 and it is unchanged by including the self-generated magnetic field. We prove the first correction term to this energy, the so-called Scott correction of the form S(aZ)Z2. The current paper extends the result of Solovej et al. [Commun. Pure Appl. Math. LXIII, 39–118 (2010)] on the Scott correction for relativistic molecules to include a self-generated magnetic field. Furthermore, we show that the corresponding Scott correction function S, first identified by Solovej et al. [Commun. Pure Appl. Math. LXIII, 39–118 (2010)], is unchanged by including a magnetic field. We also prove new Lieb-Thirring inequalities for the relativistic kinetic energy with magnetic fields.