In engineering systems design, designers iteratively go back and forth between different design stages to explore the design space and search for the best design solution that satisfies all design constraints. For complex design problems, human has shown surprising capability in effectively reducing the dimensionality of design space and quickly converging it to a reasonable range for algorithms to step in and continue the search process. Therefore, modeling how human designers make decisions in such a sequential design process can help discover beneficial design patterns, strategies, and heuristics, which are essential to the development of new algorithms embedded with human intelligence to augment the computational design. In this paper, we develop a deep learning-based approach to model and predict designers’ sequential decisions in the systems design context. The core of this approach is an integration of the function-behavior-structure (FBS) model for design process characterization and the long short-term memory unit (LSTM) model for deep leaning. This approach is demonstrated in two case studies on solar energy system design, and its prediction accuracy is evaluated benchmarking on several commonly used models for sequential design decisions, such as the Markov Chain model, the Hidden Markov Chain model, and the random sequence generation model. The results indicate that the proposed approach outperforms the other traditional models. This implies that during a system design task, designers are very likely to rely on both short-term and long-term memory of past design decisions in guiding their future decision-making in the design process. Our approach can support human–computer interactions in design and is general to be applied in other design contexts as long as the sequential data of design actions are available.