Missing marker information is a common problem in Motion Capture (MoCap) systems. Commercial MoCap software provides several methods for reconstructing incomplete marker trajectories; however, these methods still rely on manual intervention. Current alternatives proposed in the literature still present drawbacks that prevent their widespread adoption. The lack of fully automated and universal solutions for gap filling is still a reality. We propose an automatic frame-wise gap filling routine that simultaneously explores restrictions between markers’ distance and markers’ dynamics in a least-squares minimization problem. This algorithm constitutes the main contribution of our work by simultaneously overcoming several limitations of previous methods that include not requiring manual intervention, prior training or training data; not requiring information about the skeleton or a dedicated calibration trial and by being able to reconstruct all gaps, even if these are located in the initial and final frames of a trajectory. We tested our approach in a set of artificially generated gaps, using the full body marker set, and compared the results with three methods available in commercial MoCap software: spline, pattern and rigid body fill. Our method achieved the best overall performance, presenting lower reconstruction errors in all tested conditions.