On May 27, 1905, McInnes was appointed to the office of Commissioner in the Yukon Territory. His term in office was said to be one of reform and stability, in contrast to the term of his predecessor, Frederick Tennyson Congdon. He was said to be one of the most popular politicians in the Yukon in the early 1900s. However, on December 31, 1906, McInnes had resigned and looking to sit once again in the House of Commons. J. T. Lithgow took over as Acting Commissioner until a successor to McInnes could be appointed. McInnes never again sat in the House. He tried in 1908, 1917 and 1921, only to be defeated on all occasions. He was also an unsuccessful candidate in the 1907 and 1920 BC provincial elections.
In 1909, McInnes became a judge when he was appointed to the County Court of Vancouver between 1909 and 1917. He served as police magistrate for ten years, beginning in 1944, and was known for the severity of his sentences.
William Wallace Burns McInnes died in Vancouver in 1954.