The $k$-token graph $F_k(G)$ of a graph $G$ is the graph whose vertices are the $k$-subsets of vertices from $G$, two of which being adjacent whenever their symmetric difference is a pair of adjacent vertices in $G$. In this paper, we propose a general method to find the spectrum and eigenspaces of the $k$-token graph $F_k(C_n)$ of a cycle $C_n$. The method is based on the theory of lift graphs and the recently introduced theory of over-lifts. In the case of $k=2$, we use continuous fractions to derive the spectrum and eigenspaces of the 2-token graph of $C_n$.