Detecting pulmonary nodules early significantly contributes to the treatment success of lung cancer. Several deep learning models for medical image analysis have been developed to help classify pulmonary nodules. The design of convolutional neural network (CNN) architectures, however, is still heavily reliant on human domain knowledge. Manually designing CNN design solutions has been shown to limit the data’s utility by creating a co-dependency on the creator’s cognitive bias, which urges the development of smart CNN architecture design solutions. In this paper, an evolutionary algorithm is used to optimise the classification of pulmonary nodules with CNNs. The implementation of a genetic algorithm (GA) for CNN architectures design and hyperparameter optimisation is proposed, which approximates optimal solutions by implementing a range of bio-inspired mechanisms of natural selection and Darwinism. For comparison purposes, two manually designed deep learning models, FractalNet and Deep Local-Global Network, were trained. The results show an outstanding classification accuracy of the fittest GA-CNN (91.3%), which outperformed both manually designed models. The findings indicate that GAs pose advantageous solutions for diagnostic challenges, the development of which may to be fully automated in the future using GAs to design and optimise CNN architectures for various clinical applications.