The Ice, Cloud, and land Elevation Satellite-2 (ICESat-2) and its sole scientific instrument, the Advanced Topographic Laser Altimeter System (ATLAS), was launched on 15 September 2018 with a primary goal of measuring changes in the surface of the Earth’s land ice (glaciers and ice sheets). ATLAS is a photon-counting laser altimeter, which records the transit time of individual photons in order to reconstruct surface height along track. The ground-track pattern repeats every 91 days such that changes in ice sheet surface height can be estimated through time. In this paper, we describe the set of algorithms that have been developed for ICESat-2 to retrieve ice sheet surface height from the geolocated photons for the Land Ice Along-Track Height Product (ATL06), and demonstrate their output and performance using a synthetic dataset over various land-ice surfaces and under different cloud conditions. We show that the ATL06 algorithm is expected to perform at the level required to meet the ICESat-2 science objectives for land ice.