Flocking control of multi-agents system is challenging for agents with partially unknown dynamics. This paper proposes an online learning-based controller to stabilize flocking motion of double-integrator agents with additional unknown nonlinear dynamics by using Gaussian processes (GPs). Agents interaction is described by a time-invariant infinitesimally minimally rigid undirected graph. We provide a decentralized control law that exponentially stabilizes the motion of the agents and captures Reynolds boids motion for swarms by using GPs as an online learning-based oracle for the prediction of the unknown dynamics. In particular the presented approach guarantees a probabilistic bounded tracking error with high probability.