The Baker cyst (BC), also known as the popliteal cyst or parameniscal cyst, is a fluid-filled sac that normally develops in the back of the knee, between the semimembranosus and medial head of the gastrocnemius. We aimed to evaluate the effectiveness of physiotherapy (10 days of treatment) that associates intermittent vacuum therapy (IVT) on the lower limbs in the treatment of the BC, respectively, in its size reduction. Sixty-five patients with knee osteoarthritis using Kellgren-Lawrence criteria and the presence of BC (ultrasonography evaluation), were divided into the Control and Vacuum groups. We collected the following features: sex, age, level of education, occupation, environment, body mass index, Knee Injury and Osteoarthritis Outcome Score, Western Ontario, and McMaster Universities Osteoarthritis Index, the Functional Independence Measurement, the Fall Risk Score, and the Visual Analog Scale were recorded at baseline and after 10 days. Both groups are similar in terms of demographic features. Regarding the clinical functional parameters, the results elicit a statistically significant change in all parameters between admission and discharge, including the echo volume at BC. Physical medicine and rehabilitation increase the autonomy of patients with BC. Clinical-functional improvement begins in the first 10 days of complex rehabilitation treatment; it is statistically significant and is not different between the two groups, which brings an additional argument for the effectiveness of conservative therapy in the treatment of BC. Although IVT has not demonstrated its superiority over classical balneo-physical therapy, additional research, and long-term monitoring are needed to provide additional arguments regarding this aspect.