The interpretation of the electrocardiogram (ECG) gives clinical information and helps in assessing heart function. There are distinct ECG patterns associated with a specific class of arrythmia. The convolutional neural network is currently one of the most commonly employed deep learning algorithms for ECG processing. However, deep learning models require many hyperparameters to tune. Selecting an optimal or best hyperparameter for the convolutional neural network algorithm is a highly challenging task. Often, we end up tuning the model manually with different possible ranges of values until a best fit model is obtained. Automatic hyperparameters tuning using Bayesian optimisation (BO) and evolutionary algorithms can provide an effective solution to current labour-intensive manual configuration approaches. In this paper, we propose to optimise the Residual one Dimensional Convolutional Neural Network model (R-1D-CNN) at two levels. At the first level, a residual convolutional layer and one-dimensional convolutional neural layers are trained to learn patient-specific ECG features over which multilayer perceptron layers can learn to produce the final class vectors of each input. This level is manual and aims to lower the search space. The second level is automatic and based on our proposed BO-based algorithm. Our proposed optimised R-1D-CNN architecture is evaluated on two publicly available ECG Datasets. Comparative experimental results demonstrate that our BO-based algorithm achieves an optimal rate of 99.95%, while the baseline model achieves 99.70% for the MIT-BIH database. Moreover, experiments demonstrate that the proposed architecture fine-tuned with BO achieves a higher accuracy than the other proposed architectures. Our optimised architecture achieves excellent results compared to previous works on benchmark datasets.