1 According to HomeAdvisor.com, the average cost nationwide to repair a swimming pool heater is about $400 to $600.2  Based on the type of repair and local pricing, however, actual repair costs could be significantly higher or lower. 3  A recommended annual pool heater tune-up costs $100 to $200.hile regular maintenance should help to stave off repairs, as with any complicated piece of machinery, a pool heater can break and require service. The cost to repair a pool heater depends on the heater type and the nature of the problem.