The computational complexity of the graph isomorphism problem is considered to be a major open problem in theoretical computer science. It is known that testing isomorphism of chordal graphs is polynomial-time equivalent to the general graph isomorphism problem. Every chordal graph can be represented as the intersection graph of some subtrees of a representing tree, and the leafage of a chordal graph is defined to be the minimum number of leaves in a representing tree for it. We prove that chordal graph isomorphism is fixed parameter tractable with leafage as parameter. In the process we introduce the problem of isomorphism testing for higher-order hypergraphs and show that finding the automorphism group of order-$k$ hypergraphs with vertex color classes of size $b$ is fixed parameter tractable for any constant $k$ and $b$ as fixed parameter.