Boneham was the 2012 Libertarian nominee for governor of Indiana, losing to Republican Mike Pence, who later became Vice President.
During Survivor: Pearl Islands, Boneham quickly became one of the most popular Survivor contestants, and was well known as a "gentle giant" for his distinctive appearance, which included a huge beard, tie-dye shirt and large size, as well as a boisterous, friendly-but-focused personality.
Boneham was a preselected member of the Drake tribe, before his arrival on the island for Survivor: Pearl Islands. For the first three episodes he was part of an alliance with Sandra Diaz-Twine, Christa Hastie, and Trish Dunn. In episode four, Boneham's tribe lost immunity, but he was kidnapped by the Morgan tribe and did not attend tribal council. He temporarily looked after a sea snake named Balboa who was the namesake of the merged tribe. In episode 6, Drake lost their third immunity challenge, and Dunn conspired with Jon Dalton, Diaz-Twine and Shawn Cohen to vote out Rupert, but Boneham was saved by Sandra and Shawn, sending Dunn home instead. After the next tribal council when Cohen was voted out, Burton Roberts from Drake and Lillian Morris from Morgan returned to the game, and both joined the Drake alliance at the merge. After two Morgan members had been eliminated, Dalton, Roberts and Morris sided with Darrah Johnson and Tijuana Bradley from the Morgan tribe and successfully voted Rupert out. On Day 27, Boneham became the tenth contestant voted out of the competition by his tribe mates in a vote of 5–2–1, he became the second member of the jury. On Day 39, Boneham cast his jury vote for Sandra Diaz-Twine who was the winner of the season.
Less than a month after Boneham returned home from the competition, he returned to compete in the All-Stars season, the only player from Pearl Islands to do so, and thus the first contestant in Survivor history to compete in two consecutive seasons. Boneham went on to finish fourth, being voted out in episode 15. After All-Stars ended a special aired called Survivor: America's Tribal Council, in which viewers were given the opportunity in a contest called "America Votes" to select one of the eighteen contestants to win one million dollars. The finalists were Boneham, Colby Donaldson, Tom Buchanan, and Rob Mariano. Boneham won the million dollars, receiving 85% of the 38 million votes cast. He spent his prize money on his family's debts, a college fund for his daughter, a new house for his family, and the creation of his charity, Rupert's Kids, which mentors troubled children.
After All-Stars ended, he appeared in national promos for Survivor: Vanuatu. Boneham also made an appearance in the third season of the Israeli version of Survivor in September 2009 as a part of a reward in a reward challenge.
Boneham returned to participate in the Survivor: Heroes vs. Villains as part of the Heroes tribe. He was a part of the Heroes alliance which consisted of himself, J.T. Thomas, Amanda Kimmel, Cirie Fields, James Clement and Candice Woodcock. The alliance successfully eliminated Stephenie Lagrossa and Tom Westman, however, Cirie was blindsided on day 11, and they voted James out on day 15 because his foot was injured. After James's elimination, the Heroes were down to 5 members, however, they won the last 3 immunity challenges. The tribes merged with 10 players remaining: 5 heroes and 5 villains. The Heroes thought that villain member Russell Hantz was on their side. However, Sandra warned Rupert that Russell is not with them which concerned Rupert. At tribal council, the heroes voted against villains member Jerri Manthey while the villains voted against JT, However, Parvati Shallow used one of her hidden immunity idols on Sandra, and used J.T.'s hidden immunity idol which he gave to Russell right before the merge on Jerri. Jerri's votes were negated by the idol so J.T. was blindsided thus putting the Heroes in the minority. Candice flipped to the villains side at the next tribal council so Amanda was voted out. After Parvati won the next immunity challenge, Rupert put a rock in his pocket which made Russell believe it was a hidden immunity idol. So the Villains decided to split their votes between Rupert and Candice. Due to Rupert and Colby Donaldson voting against Candice, Candice was blindsided thus sparing Rupert. Rupert was spared again at the final 7 tribal council, due to Russell and Jerri siding with him to get rid of Danielle. After the loved ones challenge, Russell plotted with Rupert and Colby to get rid of Parvati and they agreed. This plan was foiled when Parvati won immunity. At tribal council Rupert and Colby voted for Sandra, but Sandra used her hidden immunity idol, however, it only negated Rupert and Colby's votes as they were the only one's who voted against her. The 4 villains voted for Rupert thus eliminating him from the game. He came in 6th place and was the 7th member of the jury. At the final tribal council, Boneham voted for Diaz-Twine along with Courtney Yates and fellow Heroes tribemates, Thomas, Kimmel, Woodcock and Donaldson to win again which she did by a 6-3-0 vote over Parvati and Russell. At the reunion show, Rupert narrowly lost the fan favorite award to Russell.
Boneham and his wife Laura competed in the show's 27th season, Blood vs. Water. This made him the second contestant in the history of the program to play the game four times, following Rob Mariano. On day 1, Rupert's wife Laura was the first member of the Tadhana tribe to be voted out. However, Rupert traded places with her and sent himself to Redemption Island in her place in order to give Laura a chance at playing the game. This sacrifice allowed Laura to play the game on the Galang tribe. Rupert ultimately lost the first duel at Redemption on day four, therefore finishing in 20th place.
Shortly after his Survivor appearances, Boneham briefly appeared at charity events sponsored by the Indiana Ice and Hardee's. In 2004 he appeared as a stable hand named Paul in "The Big My Little Pony Episode", the third season premiere of the TV series Half & Half. In 2006, he appeared in the independent movie Open Mic'rs. He also made a cameo appearance as a homeless man in "The Radford Reshuffle", the sixth season premiere of the show Yes, Dear. Boneham also makes an appearances as an extra in the bar fight scene in A Million Ways to Die in the West.
In 1983, before appearing on Survivor, Boneham worked with mentally handicapped children in Abilene, Texas. He then moved to Indiana to work with troubled young adults. In 1991, he purchased an abandoned house and converted it into a vocational training center for young adults who had been expelled from school.
After being awarded one million dollars on Survivor: America's Tribal Council, Boneham used a large percentage of his winnings to establish Rupert's Kids, to help "at-risk teens". The organization joined with the City of Indianapolis to create the Park Adoption Program.
On August 30, 2011, Boneham announced that he would consider running for governor of Indiana. He launched his campaign on October 22, declaring that he would seek the nomination of the Libertarian Party. He won their nomination and ran against Republican nominee Mike Pence and Democratic nominee John R. Gregg. Incumbent Republican Governor Mitch Daniels was term-limited.
Boneham wrote on his official website, "I have spent my entire adult life serving my community and I see an opportunity to make a difference for Indiana", referencing his troubled-youth charity, Rupert's Kids. "While surveying the current choices for our next Governor, I do not see anyone that has an understanding of what daily life is like for many Hoosiers nor anyone who appears to understand the harm that misguided government policies are doing to our communities. It is obvious that career politicians are not the answer because they are often the problem. I will be evaluating whether or not hardworking Hoosiers are ready for a new voice with new ideas." He states that he has been a Libertarian for more than 20 years, but did not become active in the party until 2012.
Boneham and running mate Brad Klopfenstein received 101,868 votes, 3.95 percent of the total.