The south-east Indian Ocean population of pygmy blue whales (Balaenoptera musculus brevicauda) forages in habitats between temperate foraging grounds off southern Australia and breeding grounds in Indonesian waters. With the opportunity to forage during migration, limited seasonal variation in body condition would be expected. However, increasing numbers of individuals in poor body condition with prominent spinal columns and other features of emaciation have been sighted during their southern migration. This study aimed to measure the morphology and body condition (relative body volume to body length) of pygmy blue whales during their northbound and southbound migration. Unmanned aerial vehicles were used to obtain images of 42 pygmy blue whales (one calf, five juveniles and 36 adults, including one lactating female) in 2021 and 2022. The body lengths ranged from 15.32 to 24.32 m, and the mean relative head length, length to blowhole, width of eyes, fluke width and length of peduncle were 21.8, 18.1, 12.8, 22.9 and 21.3% respectively. There was a significant decrease in body condition of 15.3% between north and southern migrating adult whales. Given the importance of body condition for reproductive success, understanding if this loss is due to natural seasonal variation, or habitat or prey disturbance from environmental environmental or anthropogenic sources, has implications for the future management of the species.