An inverse source problem for a non-automonous time fractional diffusion equation of order \((0<\beta <1)\) is considered in a bounded Lipschitz domain in \(\mathbb {R}^d\). The missing solely time-dependent source is recovered from an additional integral measurement. The existence, uniqueness and regularity of a weak solution is studied. We design two numerical algorithms based on Rothe’s method over uniform and graded grids, derive a priori estimates and prove convergence of iterates towards the exact solution. An essential feature of the fractional subdiffusion problem is that the solution lacks the smoothness near the initial time, although it would be smooth away from \(t = 0\). Rothe’s method on a uniform grid addresses the existence of a such a solution (non-smooth with \(t^\gamma \) term where \(1>\gamma > \beta \)) under low regularity assumptions, whilst Rothe’s method over graded grids has the advantage to cope better with the behaviour at \(t=0\) (also here \(t^\beta \) is included in the class of admissible solutions) for the considered problems. The theoretical obtained results are supported by numerical experiments and stay valid in case of smooth solutions to the problem.