The agency's mandates are specified under RA 8044 ("Youth in Nation-Building Act of 1995") and RA 10742 ("SK Reform Act of 2015").
The agency convenes the National Youth Parliament (NYP) every two years. The NYP is a 3-day convention of youth leaders wherein policy recommendations are formulated to address youth issues, and serve as the government's guide in policy formulation and program development. Started in 1996, youth leaders gather every two years to share ideas and gain valuable insights and networks to aid them in their youth development efforts. The most recent parliament was held last October 2018 in Davao City, where it caught controversies due to alleged electioneering.
The agency serves as the National Secretariat of the Sangguniang Kabataan (SK), local youth councils in the Philippines. The agency conducts mandatory continuing program for elected SK officials and coordinates with relevant government agencies for policies involving the SK and Local Youth Development Offices. In coordination with various youth groups, the agency spearheaded efforts for the passage of RA 10742 in 2018.
The agency is mandated to formulate, approve, and implement Medium-Term Youth Development Program (MTYDP) every three years. Currently, the MTYDP in place is called the Philippine Youth Development Plan for 2017-2022. It is also mandated to conduct a study on the situation of the youth sector every three years to identify priority needs, prevailing attitudes, and gaps in service delivery. Its most recent study is entitled the National Youth Assessment Study (NYAS) conducted in 2015.
The agency contributes to the development and proliferation of youth organizations in the country. The agency's Youth Organization Registration Program (YORP) was launched to register, help, and facilitate the establishment of youth organizations and youth-serving organizations.

The agency also founded the Ten Accomplished Youth Organizations (TAYO) Awards, an annual search and recognition program for outstanding contributions made by youth and youth-serving organizations nationwide. Under the term of NYC Chairperson Ronald Cardema, the agency stopped sponsoring the award-giving program establish the "President Rodrigo Roa Duterte Youth Leadership Awards", which did not materialize.

The National Youth Volunteer Program, initially established to mobilize youth volunteers for the 2005 Southeast Asian Games, is now an ongoing platform for volunteer training and mobilization for various activities nationwide.

In October 2018, the 12th National Youth Parliament held in Davao City was met by a series of controversies. First, then-NYC Chairperson Ronald Cardema was criticized for openly accusing youth groups Kabataan Partylist and Anakbayan as communist recruiters during the program's orientation.

On the first day of the event, the program was suspended to accommodate then-senatorial candidate Bong Go, who discussed his campaign platform and invited delegates to support his campaign. Delegates were asked to do the "Duterte fist-pump" pose during a photo opportunity, while SK Federation Presidents were invited to celebrate with Go in the evening. In response, delegates passed a resolution barring politicians from using the event for political campaigns. Likewise, various youth groups and alumni of the parliament released statements criticizing the agency. In a Facebook post, Go denied allegations that he attended the event for his political campaign.
On March 23, 2020, the agency released a statement addressed to Senate President Vicente "Tito" Sotto III, manifesting its support for the immediate passage of a legislative measure granting additional powers to President Rodrigo Duterte for COVID-19 response. This was met by criticism from youth and civil society groups as the initial bill contained provisions deemed unconstitutional. The agency's employees association called NYCEA released a statement clarifying that the statement did not go through any form of consultation with youth stakeholders or other NYC officials. In response, NYC Chairperson Enriquez threatened the NYCEA Board with disciplinary action for misconduct and insubordination as stated in the NYC Memorandum dated March 31, 2020 and April 13, 2020.

In June 2020, the agency's employees association sent a letter addressed to President Rodrigo Duterte citing NYC Chairperson Enriquez's "abuse and usurpation of authority, violation of security of tenure, and harassment". In support, more than 120 SK chapters and youth groups released a statement calling for the Enriquez' resignation for "failure to release statements or action points to address pressing issues faced by the youth sector [amid the COVID-19 pandemic]" and for using the agency's social media accounts to release support towards the proposed Anti-Terrorism Bill. Neither Enriquez nor the Office of the President responded to the issues.
In an audit report released in 2022, the Commission on Audit flagged the NYC under Ronaldo Cardema for illegally diverting up to P2.714 million in 2021 to support the National Task Force to End Local Communist Armed Conflict. The funds were meant for the training of youth leaders under the Sangguniang Kabataan Mandatory and Continuing Training Fund and Marawi City rehabilitation efforts through Task Force Bangon Marawi.

• Media related to National Youth Commission (Philippines) at Wikimedia Commons
• National Youth Commission Philippines website