The park was initially built as a cemetery for the municipality of Manila during the Spanish colonial period. During this time, the Spanish intended Paco Park as a cemetery for wealthy Spanish families residing in Intramuros at that time. Many wealthy Spaniards interred their loved ones' remains inside the park after it was built in the late 1700s.
Then, in 1822, when the cholera epidemic struck Manila, its victims were also interred in Paco Park. As Manila's population increased, the park was expanded, adding a second outer wall with its tops made into pathways for promenades. Later on, a Roman Catholic chapel was added to the Paco Park's inside walls and was devoted to St. Pancratius. The Philippines' national hero Dr. Jose Rizal was also once buried at the park. Dr. Jose Rizal was interred at the park after being executed in Bagumbayan on December 30, 1896. Today, a shrine to Dr. Jose Rizal has been added inside Paco Park. Years later, in 1912, the park ceased to be a burial ground, and its remains were transferred.
No remarkable events happened at Paco Park until the Second World War when the Japanese forces made the park their central depot for ammunition and other supplies. With the park's high walls, the area became the Japanese forces' ideal position for defense. The Japanese dug several trenches around and within Paco Park, which were later abandoned when Manila was liberated in 1945.
Then, in 1966, Paco Park was declared a national park. In that year, the park's old grandeur, which was ruined in the Second World War, was gradually restored. Years later, during Marcos's presidency, the park was chosen as one location for cultural events. In 1980, classical concerts started to be held at the park, as part of the Philippine-German month celebrations. Today, Paco Park presents events that continue to be well-attended.