He served as the 22nd chief justice of the Supreme Court of the Philippines from December 8, 2006, by President Gloria Macapagal Arroyo until his mandatory retirement on May 17, 2010.

In 1969, he joined the law practice of his elder brother Isaac, a future judge whose murder at age 42 remains unsolved to date.

His predecessor as Chief Justice, Artemio Panganiban, once lauded Puno's writing in the following manner: "Like a trained surgeon, he uses his pen with razor-like precision to separate the excise fabrication from truth and pretension from reality.

[8] On January 7, 2008, the Social Weather Stations (November 30 to December 3, 2007) survey released the performance rating of Chief Justice Reynato Puno - 32% satisfied and 34% dissatisfied, or net –2, having been in single digit since March 2007.

[16][17] The 22nd Puno Supreme Court held a National Consultative Summit on extrajudicial killings on July 16 and 17, 2007 at the Manila Hotel.

Invited representatives from the three branches of the government participated (including the AFP, the PNP, CHR, media, academe, civil society and other stakeholders).

Director Geary Barias, chief of the police's anti-killings Task Force Usig, Sen. Panfilo Lacson, Manila Mayor Alfredo Lim, Caloocan Bishop Deogracias Yñiguez, reelected party-list Representatives Satur Ocampo (Bayan Muna) and Crispin Beltran (Anakpawis) graced the affair.

SC Chief Justice Reynato Puno said that the "National Consultative Summit on Extrajudicial Killings and Forced Disappearances: Searching for Solutions," would help stop the murders.

Yniguez scored the government for failing to actively pursue investigations on the hundreds of killings, and the Catholic Church was alarmed that victims have been deprived of their "fundamental right" to live.

Yniguez similarly criticized the government's alleged insistence to implement its Oplan Bantay Laya I and II, the military's counter-insurgency operation-plans which militants have said consider legal people's organizations as targets.

Meanwhile, Bayan urged the Supreme Court to "check serious threats to civil liberties and basic freedoms" including the anti-terror law or the Human Security Act of 2007, which took effect on July 15 despite protests from leftist groups.

Vice President Teofisto Guingona Jr. joined Bayan and other leftist groups as petitioners in their formal pleading before the Supreme Court challenging the constitutionality of the law.

Bayan chair Carol Araullo said the respondents included members of the Anti-Terrorism Council headed by Executive Secretary Eduardo Ermita and Raul Gonzalez.

Among the other recommendations of the summit are: -- for the Supreme Court to reexamine the case of Umil v. Ramos, which said rebellion and related crimes are continuing offenses, thus allowing the warrantless arrest of suspects; to carefully study the possibility of creating a new offense for the killings and assaults on journalists, judges and activities, akin to the law penalizing violence against woman and children; the establishment of sanctuaries where victims and witnesses can take refuge; for the President to certify and the Senate to ratify the Rome Statute, which established the International Criminal Court, and Protocol 1 of the Geneva Convention, which addresses the issue of making civilian populations or individual civilians the object of attacks; the enactment of a law addressing and accurately defining extrajudicial killings and enforced disappearances; a study on the use of the writ of Amparo for greater protection of Constitutional rights, and a more creative and resourceful application of the writ of habeas corpus; suspending the presumption of regularity in the performance of official duty in cases of extrajudicial killings and enforced disappearance; studying whether the government can continue invoking its immunity from suspension in cases of extrajudicial killings and enforced disappearances; allowing petitioners for the writ of habeas corpus to seek court orders to search the premises of police and military camps and stations in the presence of a representative from the Commission on Human Rights; requiring the Department of Interior and Local Government (DILG) to take DNA samples of unidentified cadavers for preservation in the Philippine National Police laboratory; the adoption of international standards of command responsibility; the enhancement of moral, ethical and constitutional values that put a premium on tolerance and the rule of law.

Baesa, who was based in Irosin, Albay, was responsible for organizing the death squads which carried out the killings of Max Frivaldo, Ding Uy, Rei Mon Guran and Barangay Chairman Neal Futalan.

Further, former vice president Teofisto Guingona and BAYAN petitioned the Court to declare the Human Security Act (HSA) unconstitutional.

Other petitioners were Gabriela, Kilusang Magbubukid ng Pilipinas, Movement of Concerned Citizens for Civil Liberties, state workers' group COURAGE, Kadamay, Solidarity of Cavite Workers, League of Filipino Students, HEAD, Anakbayan, Pamalakaya, Alliance of Concerned Teachers, Migrante and AGHAM.

[21][22][23] Twin horrible deaths happened on / circa the same day last year, January 15, 2007, that the Supreme Court of the Philippines' (logo or seal) was mysteriously burned into halves by an almost one-hour afternoon fire.

In February 1997, another OMI leader, Bishop Benjamin de Jesus was shot dead in front of the Jolo cathedral.

[27] In 2006, the Asian Human Rights Commission stated that there had been 26 priests, pastors, and churchmen who were liquidate or were victims of violence under the Gloria Macapagal Arroyo administration since 2001.

[29] On August 17, 2007, Puno said that the writ of amparo (Spanish for protection), would strip the military of the defense of denial (Volunteers Against Crime and Corruption's 9th anniversary celebration at Camp Crame).

This rule empowers our courts to issue reliefs that may be granted through judicial orders of protection, production, inspection and other relief to safeguard one's life and liberty The writ of amparo shall hold public authorities, those who took their oath to defend the constitution and enforce our laws, to a high standard of official conduct and hold them accountable to our people.

The sovereign Filipino people should be assured that if their right to life and liberty is threatened or violated, they will find vindication in our courts of justice.

[37] On September 28, 2007, the Asian Human Rights Commission (AHRC) commented that the Writ of Amparo and Habeas Data (Philippines) was insufficient: "Though it responds to practical areas it is still necessary that further action must be taken in addition to this.

Puno announced that his Court would hold the 2nd summit, dubbed as "Forum on Increasing Access to Justice: Bridging Gaps and Removing Roadblocks," which were held simultaneously in 3 venues in Luzon, the Visayas and Mindanao from June 30 to July 1, 2008, via videoconferencing.

"[45] Rule of Law Effectiveness (RoLE) Project of CMIS aims "to (1) reduce delay and prevent case congestion, as well as to generally speed up the pace of litigation, (2) strengthen judicial accountability and its integrity infrastructure, (3) enhance the capacity of Justices to manage caseload more efficiently and in a more convenient manner, (4) improve access to justice and public access to relevant information on cases, and (5) improve capacities for sound oversight planning, monitoring, and evaluation of court operations and performance and support better supervision of court operations.

The Rule was promulgated by the Supreme Court of the Philippines pursuant to its "Increasing Access to Justice Program" with support funds from the United States Agency for International Development and the American Bar Association–Rule of Law Initiative.