As a result of fatigue, bone sustains microdamage, which is then repaired by bone‐remodeling processes. How osteoclastic activity is targeted at the removal of microdamaged regions of bone matrix is unknown. In the current studies, we tested the hypothesis that changes in osteocyte integrity, through the initiation of regulated cell death (apoptosis), are associated with fatigue‐related microdamage and bone resorption. Ulnae of adult rats were fatigue‐loaded to produce a known degree of matrix damage. Osteocyte integrity was then assessed histomorphometrically from terminal deoxynucleotidyl transferase–mediated deoxyuridine triphosphate–nick end labeling (TUNEL)–stained sections to detect cells undergoing DNA fragmentation associated with apoptosis;​ toluidine blue–stained sections were used for secondary morphological confirmation. Ten days after loading, large numbers of TUNEL‐positive osteocytes were found in bone surrounding microcracks and in bone surrounding intracortical resorption spaces (∼300% increases over controls, p < 0.005). TUNEL labeling in loaded ulnae at sites distant from microcracks or resorption foci did not differ from that in control bone. Osteocytes in toluidine blue–stained sections showed equivalent trends to TUNEL‐stained sections, with significant increases in pyknotic nuclei and empty lacunae associated with microcracks and intracortical resorption spaces. TUNEL‐positive osteocytes were observed around bone microdamage by 1 day after loading (p < 0.01 relative to baseline), and their number remained elevated throughout the entire experimental period. Increases in empty lacunae and decreases in normal osteocyte numbers were observed over time as well. These studies show that (1) osteocyte apoptosis is induced by bone fatigue, (2) this apoptosis is localized to regions of bone that contain microcracks, and (3) osteoclastic resorption after fatigue also coincides with regions of osteocyte apoptosis. The strong associations between microdamage, osteocyte apoptosis, and subsequent bone remodeling support the hypothesis that osteocyte apoptosis provides a key part of the activation or signaling mechanisms by which osteoclasts target bone for removal after fatigue‐induced matrix injury.