Context: Increasing rates of habitat fragmentation globally underscore the importance of understanding the full spectrum of fragmentation’s ecological consequences. Fragmentation alters the thermal environment of fragments, which may alter the body size of ectothermic organisms and in turn impact survival and reproduction. Objectives: To determine whether experimental habitat fragmentation alters body size in the heliothermic, ground-dwelling common garden skink (Lampropholis guichenoti). Methods: We use body size data spanning 29 years to experimentally test the prediction that lizards will experience morphological changes in forest fragments but not in non-fragmented controls. Results: Lizards were smaller in forest fragments relative to those in the non-fragmented controls after the fragmentation treatment was applied. For lizards within forest fragments, the greater the exposure to deforested areas, the greater the decline in body size. This pattern was strongest in the first 5 years following fragmentation and weakened or reversed over time as the pine plantation matrix surrounding the fragments matured. Using sampling site-scale temperature data for the most recent 5 years of the experiment, we show that temperature predicts lizard body size. Our findings are consistent with predictions made under the temperature-size rule that ectotherms will be smaller in fragmented landscapes because of temperature increases at newly created edges. Conclusions: Our results raise new concerns about the effects of fragmentation on organisms in remnant patches and offer new research priorities, as more evidence is needed to determine the generality of body size declines in fragmented landscapes. Our results also highlight that body size declines, often attributed to climate change, may be amplified by habitat fragmentation, which has been global in its impact.