The planetary boundary layer height (PBLH) is an important meteorological feature defining the boundary between surface processes and the free troposphere. The PBLH plays a key role in cloud formation and the vertical extent of aerosols and air pollutants. Measurements of PBLH were made by meteorological sensors mounted to a multi-copter drone over the southern Great Barrier Reef, Australia. We then compared these drone-based measurements to remote-sensed PBLH observations, using a Mini-Micropulse (MP) LiDAR system. Across the measurement campaign (1 March–2 April 2023), the mean PBLH value using the drones was 801 ± 203 m. Using the gradient method for MP LiDAR normalised relative backscatter profiles, the mean PBLH was 811 ± 260 m. Using an ideal MP LiDAR profile fitting method the mean was 912 ± 202 m and using a wavelet covariance transform method the mean was 862 ± 298 m. The boundary layer was consistently well mixed, without convective instability or a strong diurnal PBLH cycle. The three MP LiDAR methods compared well to the drone measurements overall with Pearson’s R correlation coefficients >0.60; however, estimates from the MP LiDAR were typically ~10% higher than from the drone. These results indicate congruence between the backscatter- and thermodynamically derived PBLH at One Tree Island, which is robust to variations in sampling conditions and the choice of MP LiDAR PBLH retrieval method.