In this work, a machine translation framework is proposed to tackle the flight plan generation in the air transport field. Diverging from the traditional human expert‐based way, a novel sequence‐to‐sequence transfer transformer network to automatic flight plan generation with enhanced operational acceptability is presented. It allows the user to translate the departure and arrival airport pairs denoted as test sentences, into the flyable waypoint sequences denoted as the corresponding source sentences. The approach leverages deep neural networks to autonomously learn air transport specialized knowledge and human expert insights from industry legacy data. Moreover, a multi‐head attention mechanism is adopted to model the complex correlation between airport pairs. Besides, we introduce an innovative waypoint embedding layer to learn effective embeddings for waypoint sequences. Additionally, an extensive flight plan dataset is constructed utilizing real‐world data in China spanning from July to September 2019. Employing the proposed model, rigorous training and testing procedures are conducted on this dataset, yielding remarkably favourable outcomes based on automatic evaluation metrics that are BLEU and METEOR, which outperform other popular approaches. More importantly, the proposed approach achieves high performance in the operational validation and visualization, showing its application potential for real‐world air traffic operation.