Purpose: Energy expenditure is a key parameter in quantifying physical activity. Traditional methods are limited because they are expensive and cumbersome. Additional portable and cheaper devices are developed to estimate energy expenditure to overcome this problem. It is essential to verify the accuracy of these devices. This study aims to validate the accuracy of energy expenditure estimation by a respiratory magnetometer plethysmography system in children, adolescents and adults using a deep learning model. Methods: Twenty-three healthy subjects in three groups (nine adults (A), eight post-pubertal (PP) males and six pubertal (P) females) first sat or stood for six minutes and then performed a maximal graded test on a bicycle ergometer until exhaustion. We measured energy expenditure, oxygen uptake, ventilatory thresholds 1 and 2 and maximal oxygen uptake. The respiratory magnetometer plethysmography system measured four chest and abdomen distances using magnetometers sensors. We trained the models to predict energy expenditure based on the temporal convolutional networks model. Results: The respiratory magnetometer plethysmography system provided accurate energy expenditure estimation in groups A (R2 = 0.98), PP (R2 = 0.98) and P (R2 = 0.97). The temporal convolutional networks model efficiently estimates energy expenditure under sitting, standing and high levels of exercise intensities. Conclusion: Our results proved the respiratory magnetometer plethysmography system’s effectiveness in estimating energy expenditure for different age populations across various intensities of physical activity.