Neomorphic, membrane-associated skeletal rods are found in disparate vertebrate lineages, but their evolution is poorly understood. Here we show that one of these elements—the calcar of bats (Chiroptera)—is a skeletal novelty that has anatomically diversified. Comparisons of evolutionary models of calcar length and corresponding disparity-through-time analyses indicate that the calcar diversified early in the evolutionary history of Chiroptera, as bats phylogenetically diversified after evolving the capacity for flight. This interspecific variation in calcar length and its relative proportion to tibia and forearm length is of functional relevance to flight-related behaviors. We also find that the calcar varies in its tissue composition among bats, which might affect its response to mechanical loading. We confirm the presence of a synovial joint at the articulation between the calcar and the calcaneus in some species, which suggests the calcar has a kinematic functional role. Collectively, this functionally-relevant variation suggests that adaptive advantages provided by the calcar led to its anatomical diversification. Our results demonstrate that novel skeletal additions can become integrated into vertebrate body plans and subsequently evolve into a variety of forms, potentially impacting clade diversification by expanding the available morphological space into which organisms can evolve.