During the academic year 1987-88, prior to announcing that he would not seek re-election, Penner was a visiting fellow in the School of Political Science at Queen's University.
He also continued to write and speak of the need for Indigenous Self-Government as a Distinct Order of Government in Canada.
In 2009, Penner worked with the Algonquins of Barrier Lake in Quebec in an effort to assist them in the re-establishment of their Traditional Government.
Those who sought the return of Traditional Government lost the case, but Penner's work earned praise in the Decision and with the Algonquin people of Barrier Lake.
Recently, Penner has been invited to participate in a First Nations' Think Tank called the Yellowhead Institute of Ryerson University.
In 2010, Penner was the recipient of the Distinguished Service Award of the Canadian Association of Former Parliamentarians, cited in particular for his "continued interest and activity in the promotion of education, aboriginal rights and parliamentary democracy in Canada and abroad.