We show how to apply the macroscopic fluctuation theory (MFT) of Bertini, De Sole, Gabrielli, Jona-Lasinio, and Landim to study the current fluctuations of diffusive systems with a step initial condition. We argue that one has to distinguish between two ways of averaging (the annealed and the quenched cases) depending on whether we let the initial condition fluctuate or not. Although the initial condition is not a steady state, the distribution of the current satisfies a symmetry very reminiscent of the fluctuation theorem. We show how the equations of the MFT can be solved in the case of non-interacting particles. The symmetry of these equations can be used to deduce the distribution of the current for several other models, from its knowledge for the symmetric simple exclusion process. In the range where the integrated current $Q_t ∼ \sqrt{t}$, we show that the non-Gaussian decay $\exp [- Q_t^3/t]$ of the distribution of $Q_t$ is generic. ; Comment: 17 pages, 2 figures