Understanding the impacts of endemic parasites on protected hosts is an essential element of conservation management. However, where manipulative experiments are unethical, causality cannot be inferred from observational correlative studies. Instead, we used an experimental structure to explore temporal associations between body condition of a protected reptile, the tuatara (Sphenodon punctatus) and infestation with ectoparasites (ticks and mites). We surveyed tuatara in a mark-recapture study on Stephens Island (New Zealand), which encompassed the pre-peak, peak and post-peak infestation periods for each ectoparasite. Tick loads during the peak infestation period were negatively related to body condition of tuatara. Body condition before the peak was not related to subsequent infestation rates; however, tick loads in the peak were negatively related to subsequent changes in body condition. Mite loads during the peak infestation period were not correlated with body condition of tuatara. Body condition before the peak had no effect on subsequent mite infestation rates, but mite loads of small males during the peak were negatively related to subsequent changes in body condition. Our results suggest that both ectoparasites reduce the body condition of tuatara, which has implications for the long-term conservation management of this host and its parasites.