Lifetime estimation of lead–acid batteries in stand-alone photovoltaic (PV) systems is a complex task because it depends on the operating conditions of the batteries. In many research simulations and optimisations, the estimation of battery lifetime is error-prone, thus producing values that differ substantially from the real ones. This error can indicate that the “optimal” system selected by the optimisation tool will not be optimal. In this paper, all of the components of a PV system have been considered simultaneously to simulate the behaviour of the system. One of these important components is the battery charge controller, which significantly affects the lifetime of batteries. The results of the simulations have allowed a comparison of the most common methods of battery lifetime prediction used by simulation and/or optimisation tools with a weighted Ah-throughput method developed a few years ago. The results show that this recent method provides more accurate lifetime values. In a simulation of a real off-grid household PV system where the real battery lifetime was 6.2years, the weighted Ah-throughput model predicted a lifetime of 5.8years; however, the other methods obtained lifetimes of more than 15years. In a simulation of another PV system designed to supply the load of an alarm where the real batteries lifetime was 5.1years, the weighted Ah-throughput model predicted a lifetime of 4.4years; however, the other methods obtained lifetimes of more than nine years.