(1) Background: Working from home is becoming increasingly common and has many advantages, but also negative consequences such as reduced physical activity, poor ergonomics and stress. Many people find it difficult to attend in-person rehabilitation sessions due to transportation barriers and limited access to rehabilitation facilities. Therefore, the aim of our study was to investigate whether our online preventive exercise programme effectively improves the musculoskeletal and mental health of sedentary workers. (2) Methods: The study participants worked from home on a long-term basis. Our research group consisted of 30 people, 16 in the intervention group and 14 in the control group. The intervention group members participated in a complex preventive exercise programme three times a week for 10 weeks. The training took place online. Before and after the exercise programme, various tests were used to assess the functional status of the participants’ spine, the strength and flexibility of their core muscles (Core, Kempf and Kraus–Weber tests) and their mental state (Beck Depression Inventory). (3) Results: Significant improvement was observed in the intervention group in the Core, Kempf, Kraus–Weber and Beck tests. (4) Conclusions: Our online complex training programme proved to be effective during the evaluation. It is crucial to tailor remote rehabilitation services to the individual needs and preferences of patients and healthcare professionals.