Immersive VR technologies offer versatile training tools by recreating real-world situations in a virtual and safe environment and allowing users to have a first-person experience. The design of such training systems requires defining the most critical components to simulate, and to what extent they can be simulated successfully. One open research question for designing such systems is how to represent the user in the virtual environment, and which is the added value of this representation for training purposes. In this work, we focus on how the user’s hand representation in an immersive virtual environment can impact the training of tool-based motor skills. To investigate this question, we have designed a VR trainer for a simple tool-based pick and place task. A user experiment was conducted to evaluate how the movements of the users’ real hand representation influence their performance and subjective experience in the virtual environment. For that purpose, the participants performed the task on the VR simulator with two conditions: the presence or absence of their animated virtual hands representation. The results of this study show that, although users prefer to have a visual representation of their hands, they achieved similar and correlated performance in the VR system regardless of the hand representation condition. These results suggest that the presence of the user’s hand representation is not necessary when performing a tool-based motor skill task in a VR trainer. These findings have practical implications for the design of VR simulators for training motor skills tasks since adding users’ hand representation may require cumbersome and expensive additional devices.