The rapid recovery of the Australian humpback whale (Megaptera novaeangliae) population and parallel increase in maritime traffic, has increased the spatial overlap between whales and vessels in Australian waters. Ship strike is a recognized global anthropogenic source of mortality or injury to large whales, and a potentially increasing risk in Australia. However, our understanding and evaluation of this threat to humpback whales around Australia, is hindered by the lack of seasonal whale distribution data in high marine traffic areas. Here, we present five consecutive years (2017–2021) of both north and south migrating humpback whale distribution data to quantify the relative risk of ship strike based on the co-occurrence with commercial ships in Moreton Bay. This marine embayment is home to Australia's fastest growing container port (The Port of Brisbane) and has recently been identified for its ecological importance to this migrating species. We quantified co-occurrence by multiplying predicted whale and ship densities together to estimate both intra- and inter-annual ship strike risk. Ship strike risk increased during the humpback whale's southern migration (September-October), coinciding with a substantial habitat shift into the Bay during this time. Groups containing calves were a predominant pod type in Moreton Bay. Given their increased vulnerability to ship strike, this study underscores the need for immediate and effective mitigation actions, such as seasonal vessel speed reductions as well as mariner education and outreach programs.