In 2006, Navajo Nation President Joe Shirley, Jr. selected Shelly as his running mate in the 2006 presidential election.

Although Navajo Nation elections are officially non-partisan, Shelly was a registered Democrat active in state politics in New Mexico, Arizona, and Utah.

He worked with the New Mexico state legislature and the governor's office to fund capital improvement projects on the Navajo Nation.

[11] In October 2010, Ben Shelly, among other Navajo tribal officials, were charged in an investigation of slush funds just weeks before the November election.

On four occasions, Shelly filed applications for discretionary funds on behalf of his family and personally approved the requests, a complaint alleged.

Tribal ethics and rules laws have limits on the value of gifts lawmakers can receive and prohibit engaging in conflicts of interest.

Police served some delegates with the complaints just before they convened for the fourth day of their fall session in the tribal capital of Window Rock.

[13] "If Shelly is found guilty, however, he will be removed from office and the people will need to launch a new election process," NM State Rep. Ray Begaye, D-Shiprock said.

[16] Despite Vice President Shelly facing criminal charges in the probe of the council's controversial use of discretionary funds, he would go on to win the 2010 election.

Shelly would serve as president during the 88-member Tribal Council reduction following the special election of December 2009 that was aimed at reforming the Navajo government.

During the Navajo Nation primary election on August 26, 2014, President Ben Shelly lost his bid for a second term with only 2,446 votes from 110 chapters.

In a controversial appointment, Ben Shelly was designated interim president; contradicting Navajo Nation Code § 1006 in resolutions referenced as CD-80-14 and CD-81-14.

[17] on May 12, 2015, Ben Shelly and Rex Lee Jim finished their one term which was unprecedentedly extended another five months, after problems with the disqualification of presidential hopeful Chris Deschenee and the ongoing special election between Joe Shirley Jr. and Russell Begaye.