The present study aimed to identify changes in echocardiographic parameters before and after three-month high-intensity interval training (HIIT) and continuous moderate-intensity training (CMT) in male employees. For this purpose, using a convenience sampling method, 33 male employees of the Islamic Republic of Iran Army (office workers with a sedentary lifestyle) aged 30 through 40 were selected. Participants were divided into three groups of HIIT, CMT, and control (11 for each group) including all anthropometric data (body fat percentage, body mass index, height, weight, and VO2 max) with no history of chronic diseases, metabolic syndrome, confirmed heart disease or congenital heart defect, and hospitalization due to chronic diseases or consumption of medication affecting cardiovascular indicators. A one-way ANOVA was conducted to compare the groups. The results demonstrated that the end-systolic volumes (ESVs) (p < 0.01) and relative wall thickness (RWT) in the CMT group (p < 0.01) and the end-diastolic volumes (EDVs) (p < 0.01), stroke volumes (SVs) (p < 0.01), end-systolic and diastolic diameters (ESD, EDD) (p < 0.01), as well as the RWT and left ventricle diastolic function (E/A ratio) in the HIIT group (p < 0.05) were significantly different before and after the 12-week training (Bonferroni correction was used for pairwise comparisons). The results revealed a significant increase in the end-systolic diameters (ESDs) of the HIIT group, whereas no such increase was observed in the ESDs of the CMT group (p < 0.51). Moreover, a significant increase was observed in left ventricular (LV) RWT and aerobic power of both training groups. The significant decrease of ESVs and the significant increase in E/A ratio, ESDs, EDDs following HIIT (two to three sessions per week) may indicate beneficial and optimal LV structural adaptations and improved LV function in nonathletes (even with a sedentary lifestyle).