After some time as a visiting professor at the University of California, San Diego, he returned to ANU from 1986 to 1992, first as a Lecturer, then as a Reader.

In the mathematical study of general relativity, Huisken and Tom Ilmanen (ETH Zurich) were able to prove a significant special case of the Riemannian Penrose inequality.

The general version of the conjecture, which is about black holes or apparent horizons in Lorentzian geometry, is still an open problem (as of 2020).

Several years later, the validity of Huisken's convergence theorems were extended to broader curvature conditions via new algebraic ideas of Christoph Böhm and Burkhard Wilking.

Instead, Huisken made use of iterative integral methods, following earlier work of the analysts Ennio De Giorgi and Guido Stampacchia.

In 1987, Huisken adapted his methods to consider an alternative "mean curvature"-driven flow for closed hypersurfaces in Euclidean space, in which the volume enclosed by the surface is kept constant; the result is directly analogous.

[HY96] The corresponding existence and convergence result of Huisken–Yau illustrates a geometric phenomena of manifolds with positive ADM mass, namely that they are foliated by surfaces of constant mean curvature.

Following work of Yoshikazu Giga and Robert Kohn which made extensive use of the Dirichlet energy as weighted by exponentials, Huisken proved in 1990 an integral identity, known as Huisken's monotonicity formula, which shows that, under the mean curvature flow, the integral of the "backwards" Euclidean heat kernel over the evolving hypersurface is always nonincreasing.

[5] Huisken and Hamilton's ideas were later adapted by Grigori Perelman to the setting of the "backwards" heat equation for volume forms along the Ricci flow.

[6] Huisken and Klaus Ecker made repeated use of the monotonicity result to show that, for a certain class of noncompact graphical hypersurfaces in Euclidean space, the mean curvature flow exists for all positive time and deforms any surface in the class to a self-expanding solution of the mean curvature flow.

Based on his monotonicity formula, Huisken showed that many of these regions, specifically those known as type I singularities, are modeled in a precise way by self-shrinking solutions of the mean curvature flow.

[9] By modifying the integral methods he developed in 1984, Huisken and Carlo Sinestrari carried out an elaborate inductive argument on the elementary symmetric polynomials of the second fundamental form to show that any singularity model resulting from such rescalings must be a mean curvature flow which moves by translating a single convex hypersurface in some direction.

[14] Huisken and Ilmanen were able to adapt these methods to the inverse mean curvature flow, thereby making the methodology of Geroch, Jang, and Wald mathematically precise.

[HI01] Hubert Bray, by making use of the positive mass theorem instead of the inverse mean curvature flow, was able to improve Huisken and Ilmanen's inequality to involve the total surface area of the boundary.