In intelligent logistics systems, predicting the Estimated Time of Pick-up Arrival (ETPA) of packages is a crucial task, which aims to predict the courier’s arrival time to all the unpicked-up packages at any time. Accurate prediction of ETPA can help systems to alleviate customers’ waiting anxiety and improve their experience. We identify three main challenges of this problem: i) Unlike the travel time estimation problem in other fields like ride-hailing, the ETPA task is distinctively a multi-destination and path-free prediction problem. ii) An intuitive idea for solving ETPA is to predict the pick-up route then the time in two stages. However, it is difficult to accurately and efficiently predict couriers’ future routes in the route prediction step since their behaviors are affected by multiple complex factors. iii) Furthermore, in the time prediction step, the requirement for providing a courier’s all unpicked-up packages’ ETPA at once in real-time makes the problem even more challenging. To tackle the above challenges, we propose RankETPA, which integrates the route inference into the ETPA prediction. First, a learning-based pick-up route predictor is designed to learn the route-ranking strategies of couriers from their massive spatial-temporal behaviors. Then, a spatial-temporal attention-based arrival time predictor is designed for real-time ETPA inference via capturing the spatial-temporal correlations between the unpicked-up packages. Extensive experiments on two real-world datasets and a synthetic dataset demonstrate that RankETPA achieves significant performance improvement against the baseline models.