In the field of motion analysis, the gold standard devices are marker-based tracking systems. Despite being very accurate, their cost, stringent working environments, and long preparation time make them unsuitable for small clinics as well as for other scenarios such as industrial application. Since human-centered approaches have been promoted even outside clinical environments, the need for easy-to-use solutions to track human motion is topical. In this context, cost-effective devices, such as RGB-Depth (RBG-D) cameras have been proposed, aiming at a user-centered evaluation in rehabilitation or of workers in industry environment. In this paper, we aimed at comparing marker-based systems and RGB-D cameras for tracking human motion. We used a Vicon system (Vicon Motion Systems, Oxford, UK) as a gold standard for the analysis of accuracy and reliability of the Kinect V2 (Microsoft, Redmond, WA, USA) in a variety of gestures in the upper limb workspace—targeting rehabilitation and working applications. The comparison was performed on a group of 15 adult healthy subjects. Each subject had to perform two types of upper-limb movements (point-to-point and exploration) in three workspace sectors (central, right, and left) that might be explored in rehabilitation and industrial working scenarios. The protocol was conceived to test a wide range of the field of view of the RGB-D device. Our results, detailed in the paper, suggest that RGB-D sensors are adequate to track the upper limb for biomechanical assessments, even though relevant limitations can be found in the assessment and reliability of some specific degrees of freedom and gestures with respect to marker-based systems.