We give a new formula for computing the isospectral reduction of a matrix (and graph) down to a submatrix (or subgraph). Using this, we generalize the notion of isospectral reductions. In addition, we give a procedure for constructing a matrix whose isospectral reduction down to a submatrix is given. We also prove that the isospectral reduction completely determines the restriction of the quantum walk transition matrix to a subset. Using these, we construct new families of simple graphs exhibiting perfect quantum state transfer.