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Abstract Vertical energy transports due to dissipating gravity waves in the mesopause region (85–100 km) are analyzed using over 400 h of observational data obtained from a narrow‐band sodium wind‐temperature lidar located at Andes Lidar Observatory (ALO), Cerro Pachón (30.25°S, 70.73°W), Chile. Sensible heat flux is directly estimated using measured temperature and vertical wind; energy flux is estimated from the vertical wavenumber and frequency spectra of temperature perturbations; and enthalpy flux is derived based on its relationship with sensible heat and energy fluxes. Sensible heat flux is mostly downward throughout the region. Enthalpy flux exhibits an annual oscillation with maximum downward transport in July above 90 km. The dominant feature of energy flux is the exponential decrease from 10⁻²to 10⁻⁴ W m⁻²with the altitude increases from 85 to 100 km and is larger during austral winter. The annual mean thermal diffusivity inferred from enthalpy flux decreases from 303 m²s⁻¹at 85 km to minimum 221 m²s⁻¹at 90 km then increases to 350 m²s⁻¹at 99 km. Results also show that shorter period gravity waves tend to dissipate at higher altitudes and generate more heat transport. The averaged vertical group velocities for high, medium, and low frequency waves are 4.15 m s⁻¹, 1.15 m s⁻¹, and 0.70 m s⁻¹, respectively. Gravity wave heat transport brings significant cooling in the mesopause region at an average cooling rate of 6.7 ± 1.1 K per day.