Experiment design for quantum channel parameter estimation includes the design of the quantum input to the channel and the observables to be applied on the resulting quantum output system, called the experiment configuration. An experiment design procedure based on maximizing the Fisher information of the qubit Pauli channel parameters is presented in this paper. It can be shown that the Fisher information is a convex function in both the input and the experiment configuration parameters. This leads to an optimal setting that includes pure input states and projective measurements directed towards the channel directions. An iterative method of estimating the channel directions is also proposed.