Due to its topological generality and flexibility, the k-ary n-cube architecture has been actively researched for various applications. However, the processor allocation problem has not been adequately addressed for the k-ary n-cube architecture, even though it has been studied extensively for hypercubes and meshes. The earlier k-ary n-cube allocation schemes based on conventional slice partitioning suffer from internal fragmentation of processors. In contrast, algorithms based on job-based partitioning alleviate the fragmentation problem but require higher time complexity. This paper proposes a new allocation scheme based on isomorphic partitioning, where the processor space is partitioned into higher dimensional isomorphic subcubes. The proposed scheme minimizes the fragmentation problem and is general in the sense that any size request can be supported and the host architecture need not be isomorphic. Extensive simulation study reveals that the proposed scheme significantly outperforms earlier schemes in terms of mean response time for practical size k-ary and n-cube architectures. The simulation results also show that reduction of external fragmentation is more substantial than internal fragmentation with the proposed scheme.