We propose a meta-learning method for modeling Hamiltonian dynamics from a limited number of data. Although Hamiltonian neural networks have been successfully used for modeling dynamics that obey the energy conservation law, they require many data to achieve high performance. The proposed method meta-learns our neural network-based model using datasets in various dynamical systems, such that our model can predict vector fields of unseen systems. In our model, a system representation is inferred from given small data using an encoder network. Then, the system-specific vector field is predicted by modeling the Hamiltonian using a Gaussian process (GP) with neural network-based mean and kernel functions that depend on the inferred system representation. This GP-based Hamiltonian allows us to analytically obtain predictions that are adapted to small data while imposing the constraint of the conservation law. The neural networks are shared across systems, which enables us to learn knowledge from multiple systems, and use it for unseen systems. In our experiments, we demonstrate that the proposed method outperforms existing methods for predicting dynamics from a small number of observations in target systems.