This paper investigates a subgradient-based algorithm to solve the system identification problem for linear time-invariant systems with non-smooth objectives. This is essential for robust system identification in safety-critical applications. While existing work provides theoretical exact recovery guarantees using optimization solvers, the design of fast learning algorithms with convergence guarantees for practical use remains unexplored. We analyze the subgradient method in this setting where the optimization problems to be solved change over time as new measurements are taken, and we establish linear convergence results for both the best and Polyak step sizes after a burn-in period. Additionally, we characterize the asymptotic convergence of the best average sub-optimality gap under diminishing and constant step sizes. Finally, we compare the time complexity of standard solvers with the subgradient algorithm and support our findings with experimental results. This is the first work to analyze subgradient algorithms for system identification with non-smooth objectives.