Joint agency, a group-level sense of agency, has been studied as an essential cognitive element while engaging in collaborative tasks. The joint agency has been actively investigated in diverse contexts (e.g., performance, reward schedules, and predictability), yet the studies were mostly conducted in real or traditional 2D computer environments. Since virtual reality (VR) is an emerging technology for remote collaboration, we aimed to probe the effects of traditional reward schedule factors with novel VR features (i.e., avatar visibility) on joint agency during remote collaboration. In this study, we implemented an experiment based on the card-matching game task to test the effect of the reward schedule (fair or equal) and the counterpart's avatar hand visibility (absent or present) on the sense of joint agency. The results showed that participants felt a higher sense of joint agency when the reward was distributed equally regardless of the individual performance and when the counterpart's avatar hand was present. There was also a significant interaction between the reward schedule and avatar visibility. In addition, joint agency, cooperativeness, reward fairness, and social presence were positively correlated to each other, with negative correlations with performance elements such as playtime, absolute score difference, absolute reward point difference, and fail count. These results indicate that both the in-game avatar stimulus and the post-game reward schedule modulate the sense of joint agency in a naturalistic VR joint task. The interaction effect of the two seemingly remote factors is derived from the different levels of perceived message understanding, which is shaped by the pre-notified reward schedule and the counterpart's avatar hand visibility.