For a prime \(p{\,>\,}3\) and a supersingular elliptic curve E defined over \(\mathbb {F}_{p^2}\) with \({j(E)\notin \{0,1728\}}\) , consider an endomorphism \(\alpha \) of E represented as a composition of L isogenies of degree at most d and assume \(L\log d = O(n)\) , where \(n{\,=\,}\log (p)\) . We prove that the trace of \(\alpha \) may be computed in \(O(n^4(\log n)^2 + dLn^3)\) bit operations, using a generalization of the SEA algorithm for computing the trace of the Frobenius endomorphism of an ordinary elliptic curve. When \(L\in O(\log p)\) and \(d\in O(1)\) , this complexity matches the heuristic complexity of the SEA algorithm. Our theorem is unconditional, unlike the complexity analysis of the SEA algorithm, since the kernel of an arbitrary isogeny of a supersingular elliptic curve is defined over an extension of constant degree, independent of p. We also provide practical speedups, including a fast algorithm to compute the trace of \(\alpha \) modulo p.