Estrada was born on February 17, 1963. He finished his primary and secondary education at the Ateneo de Manila University and earned a degree in A.B. Economics from the University of the Philippines Manila. He took up Bachelor of Laws for four years at the Lyceum of the Philippines University while serving as Vice Mayor of the then Municipality of San Juan at the age of 25. He was also bestowed an honorary Doctorate in Humanities in 2007 by the Laguna State Polytechnic University.

In 1989, Estrada married Ma. Presentacion “Precy” Vitug with whom he has four children, namely, Janella Marie, Joseph Luis Manuel, Julian Emilio and Julienne.

In 1992, he became the youngest ever elected-local chief executive in the entire nation at age 29. For three (3) consecutive terms, he administered the economic, social, political, and cultural affairs of the Municipality of San Juan beyond everyone’s expectations. He spearheaded various projects and programs for the improvement of the said municipality in the form of – construction of modernized Barangay Halls with Day Care Centers in all Barangays, repair and renovation of the now San Juan National High School, and other public elementary schools, recreation centers like gymnasiums, basketball courts and play grounds and the creation of different livelihood centers, improvement and replacement of drainages, concreting of municipal roads and the construction of a four-storey San Juan Medical Center and the San Juan Municipal Gymnasium. During his incumbency, San Juan gained the reputation of being one of the most progressive municipalities and the Most Peaceful Municipality in the Philippines.

In 2004, he was elected as senator. During his first term, he introduced at least 617 bills and resolutions and steered the passage of at least 16 bills either as principal sponsor or principal author. Jinggoy is hailed as the second most productive and prolific senator, next to Sen. Miriam Defensor-Santiago, who filed the most number of bills and resolutions in the Senate.

On July 23, 2007, Estrada was elected as Senate president pro tempore.

On August 15, 2007, the Supreme Court voted 13-0 to uphold the Sandiganbayan’s decision to grant his bail in connection with his plunder case before the graft court. His father, former president Joseph “Erap” Estrada was the main accused in that plunder case, and was subsequently convicted. However, Erap was immediately pardoned by then Pres. Gloria Macapagal-Arroyo. On September 11, 2007 Estrada introduced Senate bill 1556, proposing to make ROTC mandatory for all college students.

In 2010, he was reelected as senator, finishing in the 2nd place. During the opening of the 15th Congress on July 26, 2010, he was reelected as Senate president pro tempore.

In August 2010, Estrada claimed that while traveling to Hong Kong, he experienced a backlash of the emotions surrounding the death of 8 Chinese nationals from Hong Kong during the 2010 Manila hostage crisis. According to him, as he passed through the immigration desk in Hong Kong, officers threw back his passport at him after checking it.

A report by the Commission on Audit of the Philippines was released on August 16, 2013, showing alleged misuse of funds by lawmakers who allegedly endorsed part of their congressional allocations to bogus nongovernmental organizations. The accusations were the subject of a Senate probe that began later that month.

The Department of Justice of the Philippines filed its case against Estrada, Enrile and Revilla before the Ombudsman on September 16, 2013.

On June 23, 2014, Estrada was arrested and detained at the Philippine National Police Custodial Center in Camp Crame, Quezon City. The Philippine Senate on September 2, 2014 suspended Estrada from his Senate post for 90 days.

On September 16, 2017, Sandiganbayan anti-graft court released its resolution granting bail to Estrada.

On February 22, 2019, Estrada filed a request for a demurrer before the Sandiganbayan Fifth Division, asking the court to deviate from established procedure and to allow him to challenge the sufficiency of evidence midway into the trial. In March 2019, the court granted Estrada and his co-accused 10 days to file their respective demurrers; prosecution was also granted 10 days to respond.

On May 3, 2020, the former senator was arrested over alleged violations of the COVID-19 community quarantine rules. He said that he had been distributing relief goods to residents of the city when policemen in two patrol cars arrived at the scene and invited him to the local precinct.