Hydroxyapatite, which is the main mineral phase of mammalian bone, occurs in the form of small bricks of colloidal size organized in a way that leaves room to micro-and mesopores. These pores are filled with an electrolyte and confined fluids are recognized for manifesting different dynamical and structural behaviors when compared to bulk fluids. Research on other nanoporous materials reported that confinement may have repercussions on the effective the thermal properties of these materials. Understanding the physical origin of thermal expansion and heat capacity as a function of the hydroxyapatite porosity is, therefore, crucial to predict the thermo-mechanical behavior of bone. Molecular dynamics simulations of hydroxyapatite nanopores (2 nm  ≤  H  ≤  16 nm, where H is the size of the nanopore) in contact with liquid water have been used to determine the effect nanoporosity and water confinement on the heat capacity and thermal expansion of this important biomaterial. At temperatures corresponding to in vivo conditions, the thermal expansion of water confined in nanopores smaller than 6 nm was is solid-like but becomes liquid-like in larger nanopores. The heat capacity of confined water exhibits a maximum at pore sizes of approximately 7 nm. An up-scaling strategy taking into account the anomalous behaviour of nanoconfined water is then proposed to determine the effective heat capacity and the effective heat of hydroxyapatite expansion as a function of its porosity, and to predict regions of variability, compared with the bulk, in the thermal properties of porous hydroxyapatite.