This study proposed an algorithm called selective strategy differential evolution (SSDE) to handle the complexity of the stochastic internal task scheduling problem in cross-docking terminals. The aims of this study are to assign workers and transfer equipment to internal operations and sequence those operations under randomness and uncertainty with the purpose to minimise total tardiness. The main feature of SSDE is its ability to adapt itself in order to execute the best search strategy. The proposed algorithm was tested on 16 instances using generated data based on real-case scenarios of a pharmaceutical distribution centre. The results showed the significant performance of SSDE to other existing algorithms in terms of solution quality and computational time. The key success factors of SSDE are the use of various search strategies in a single run and the application of suitable termination conditions.