He described himself in Learning to Sing as a proud Southern Baptist who had journeyed away from those roots in his late teens in search of a religion with more liberal social policies, and then returned to that church because of family and social ties although he remains at odds with the church on some issues. When asked in a PBS Kids interview to name his idols, he responded, "When people ask me what three people I’d like to have dinner with, living or dead, I say Jesus Christ, Mr. Rogers, and Jimmy Carter."

Aiken makes it clear that he is aware not everyone shares his religious beliefs and it is not his intention to press these beliefs on others. When he worked as a camp counselor at the YMCA, he challenged other camp faculty by insisting that singing "overtly Christian songs" was inappropriate, as some of the kids were Jewish. "I stood firm... no child is going to have a spiritual crisis on my watch." His public philosophy, geared towards inclusion and service to others, reflects his stance that decisions about religion should be made at home.

Aiken has donated his time and his voice to multiple benefit events and concerts, including the 2004 Rosalynn Carter Benefit, the America's Promise Benefit, and Heather Headley's Broadway Cares/Equity Fights AIDS benefit, "Home," where he sang a duet with Headley. He was one of the celebrity readers for the Arthur Celebrity Audiobook (Stories for Heroes Series), which benefits the Bubel/Aiken Foundation (now the National Inclusion Project)and other charities, and served as spokesperson for the series. He was also a spokesperson for the 2004 Toys for Tots drive, and acted as an ambassador for the Ronald McDonald House Charities. Aiken worked with the Make a Wish Foundation to make one little boy's dream of singing on stage with Clay Aiken come true.

In September 2006, Aiken was appointed to the Presidential Committee for People with Intellectual Disabilities by President George W. Bush. Appointees serve a two-year term; Aiken was sworn in September 14, 2006 by HHS Assistant Secretary for Children and Families Wade F. Horn, Ph.D. In April 2008, Aiken told People Magazine that he was too busy to do as much as he would like, but "If there's something I can do remotely, I would've been happy to do it."

While appearing in Spamalot, Aiken used his free time and celebrity to help raise funds for Broadway Cares/Equity Fights AIDS (BC/EFA) during their fund drives and auctions. In 2010, Aiken spoke out for gay rights at the Human Rights Campaign dinner in North Carolina. He also joined other celebrities in filming an educational video for Cyndi Lauper's web based Give a Damn campaign, a project of her True Colors Fund. In addition to UNICEF and his National Inclusion Project he is promoting GLSEN, the Gay, Lesbian and Straight Education Network as one of his causes on his official website.

Aiken has been a dedicated advocate for education and for children's causes. His interest in autism issues led him, along with Diane Bubel (whose son Michael is diagnosed with autism and was tutored by Aiken), to found the National Inclusion Project (formerly the Bubel/Aiken Foundation), which supports the integration of children with disabilities into the life environment of their non-disabled peers. The Foundation runs summer camps which reflect its mission,and also presents Able to Serve awards to support the volunteer efforts of children with physical and mental disabilities. In July 2005, Raleigh's WRAL-TV reported on an internet campaign mounted by critics questioning how Aiken's foundation used its money. WRAL news hired an independent accountant who reported that program services totaled $920,000 in 2004—around 85 cents on every dollar donated—which is considered a solid percentage compared to other charities. CNN picked up the story, and Aiken appeared on Showbiz Tonight to provide details about the Foundation's programs. In late 2004, the Foundation was awarded a $500,000 grant by the US government to develop a K–12 model for inclusion in community service projects to be used in schools across the country. In addition, State Farm granted $1.5 million dollars to the Foundation to help develop a primary education curriculum focused on teaching social and life skills through service to children of all levels of ability.

On August 5, 2009, in an open letter from the founders, Clay Aiken and Diane Bubel stated "As we realized the impact the Foundation has already made, it became apparent that even bigger accomplishments could be on the horizon. To that end, we along with the rest of the Board decided that a new name for the Foundation would establish long-term credibility and stability. We sought a name that would signify the Foundation’s position as a national leader on inclusion as well as recognize the Foundation’s start and the efforts of its faithful supporters. After much thought and deliberation, we are proud to introduce the organization we co-founded as the National Inclusion Project."

In November 2004, Aiken was appointed a U.S. Fund for UNICEF National Ambassador, with a mission to help ensure that children everywhere are afforded a primary education. After the tsunami at the end of 2004, he participated in the NBC4 telethon, which raised over $10 million, and recorded public service announcements in support of South Asian tsunami relief. He later recorded a video, featuring the song "Give a Little Bit", to be used as a public service announcement to raise money for tsunami victims. He was the 2005 spokesperson for the Trick-or-Treat for UNICEF drive.

In March 2005, UNICEF sent Aiken to the tsunami-stricken Banda Aceh area to raise awareness of the need to restore education quickly to the children who survived this disaster. UNICEF sent Aiken on another mission in May 2005, to northern Uganda, to witness the plight of children called "night commuters", who flee the villages each night to sleep in streets and shelters in hopes of avoiding being kidnapped by the Lord's Resistance Army. He was sent to Kabul and Bamyan in Afghanistan in April 2007, where he was able to spend time with children in their classrooms; he also visited a health center for women and children where he administered oral polio vaccinations to babies. He observed that Afghani children, after being forbidden for so many years by the Taliban regime to attend school, are eager to return to school now that they are once again allowed to receive an education. Aiken spent his 2007 Christmas in Mexico with the children affected by the floods in the states of Chiapas and Tabasco. In late June and early July 2008, UNICEF sent Aiken to Somalia and Kenya.