Official end to the war

The Philippine Organic Act of July 1902 approved, ratified, and confirmed McKinley's Executive Order establishing the Philippine Commission and stipulated that a legislature would be established composed of a lower house, the Philippine Assembly, which would be popularly elected, and an upper house consisting of the Philippine Commission. The act also provided for extending the United States Bill of Rights to Filipinos.

On July 2 the Secretary of War telegraphed that the insurrection against the sovereign authority of the U.S. having come to an end, and provincial civil governments having been established, the office of Military governor was terminated. On July 4 Theodore Roosevelt, who had succeeded to the U.S. Presidency after the assassination of President McKinley on September 5, 1901, proclaimed a full and complete pardon and amnesty to all people in the Philippine archipelago who had participated in the conflict.

Irreconcilables

The war unofficially continued for nearly a decade as Constantino have suggested, since groups collectively know as Irreconcilables remained active. These included remnants of the Katipunan, and other resistance groups continued to their struggle by fighting the United States Military or Philippine Constabulary. After the close of the war, however, Governor-General Taft preferred to rely on the Philippine Constabulary in a law-enforcement role rather than on the American army. He was, in fact, criticized for this.

Simeon Ola of Guinobatan, Albay in the Bicol region has been suggested as the last Filipino general to surrender (on September 25, 1903) in place of Malvar.

In 1902 a veteran Katipunan member and self-proclaimed generalisimo named Macario Sakay attempted to form his own Republic, called Katagalugan after Bonifacio's, in southern Luzon. After years of resistance he was captured and executed in 1907 after accepting an amnesty offer.

Pulajanes

Quasi-religious armed groups included the pulajanes (so called because of their red garments), colorum (from a corruption of the Latin in saecula saeculorum, part of the Glory Be to the Father prayer), and Dios-Dios (literally "God-God") groups of assorted provinces. These groups were mostly composed of farmers and other poor people led by messianic leaders, and they subscribed to a blend of Roman Catholicism and folk beliefs. For example, they used amulets (called agimat or anting-anting), believing they would become bulletproof. One of these leaders was Dionisio Seguela, better known as Papa Isio (Pope Isio). The last of these groups were wiped out or had surrendered by 1913. These resistance movements were all dismissed by the American government as banditry, fanaticism or cattle rustling.

Moro Rebellion

The American government had a peace treaty with the Sultanate of Sulu at the outbreak of the war with Aguinaldo that was supposed to prevent war in Moro territory. However, after the resistance in the north was crippled, the United States began to colonize Moro land that provoked the Moro Rebellion. Beginning with the Taraca, which occurred on April 4, 1904, American forces battled Datu Ampuanagus, who surrendered after losing 200 members of his people. Numerous battles would occur after that up until the end of the conflict on June 15, 1913. During the conflict, the battles of Bud Dajo and Bud Bagsak were among the most notable since casualties included women and children.

American opposition to the war

Some Americans, notably William Jennings Bryan, Mark Twain, Andrew Carnegie, Ernest Crosby, and other members of the American Anti-Imperialist League, strongly objected to the annexation of the Philippines. Other Americans mistakenly thought that the Philippines wanted to become part of the United States. Anti-imperialist movements claimed that the United States had betrayed its lofty goals of the Spanish–American War by becoming a colonial power, merely replacing Spain in the Philippines. Other anti-imperialists opposed annexation on racist grounds. Among these was Senator Benjamin Tillman of South Carolina, who feared that annexation of the Philippines would lead to an influx of non-white immigrants. As news of atrocities committed in subduing the Philippines arrived in the United States, support for the war flagged. Mark Twain famously opposed the war by using his influence in the press. He felt it betrayed the ideals of American democracy by not allowing the Filipino people to choose their own destiny.

“There is the case of the Philippines. I have tried hard, and yet I cannot for the life of me comprehend how we got into that mess. Perhaps we could not have avoided it — perhaps it was inevitable that we should come to be fighting the natives of those islands — but I cannot understand it, and have never been able to get at the bottom of the origin of our antagonism to
the natives. I thought we should act as their protector — not try to get them under our heel. We were to relieve them from Spanish tyranny to enable them to set up a government of their own, and we were to stand by and see that it got a fair trial.

It was not to be a government according to our ideas, but a government that represented the feeling of the majority of the Filipinos, a government according to Filipino ideas. That would have been a worthy mission for the United States. But now — why, we have got into a mess, a quagmire from which each fresh step renders the difficulty of extrication immensely greater. I'm sure I wish I could see what we were getting out of it, and all it means to us as a nation.”

Some later historians, such as Howard Zinn and Daniel Boone Schirmer, cite the Philippine–American War as an example of American imperialism.

Casualties

In the official war years, there were 4,196 American soldiers dead, 1,020 of which were from actual combat; the remainderdied of disease, and 2,930 were wounded. There were also 2,000 casualties that the Philippine Constabulary suffered during the war, over one thousand of which were fatalities. It should be noted that total Filipino casualties was at the time and still is a highly-debated, argued, and politicized number. It is estimated that some 34,000 Filipino soldiers lost their lives and as many as 200,000 civilians may have died directly or indirectly as a result of the war, most due to a major cholera epidemic that broke out near its end. Philippine military deaths are estimated at 20,000 with 16,000 actually counted, while civilian deaths numbered between 250,000 and 1,000,000 Filipinos. These numbers take into account those killed by war, malnutrition, and a cholera epidemic that raged during the war. The Philippine–American War Centennial Initiative gives an estimate of 510,000 civilian deaths, and 20,000 military deaths, excluding 100,000 deaths from the Moro Rebellion. The American military and Philippine Constabulary still suffered periodic losses combating small bands of Moro guerrillas in the far south until 1913.

The high Filipino casualty figures were a combination of the superior arms and even more superior numbers of the Americans, who were equipped with the most modern, up-to-date weapons in the world, including superb Krag-Jørgensen bolt-action rifles and machine guns, and who were also well-led. Furthermore, U.S. warships stood ready to destroy Philippine positions when needed. In contrast, the Filipinos were armed with a motley collection of rifles such as Mausers and Remingtons, many which had been taken from dead enemy soldiers (including Spanish troops from the previous conflict) or smuggled into the country by their fellow Filipinos. Their artillery was not much better, consisting mostly of worn-out artillery pieces captured from the Spanish. Although they did have a few Maxim and Gatling machine guns, along with a few modern Krupp artillery pieces, these were highly prized and taken to the rear for fear of capture before they could play any decisive role. Ammunition and rifles became more scarce as the war dragged on, and Filipinos were forced to manufacture their own, like the homemade paltik. Still most did not even have firearms. Many used bolos, spears, and lances in fighting, which also contributed to high casualty figures when such obsolete weapons were used against the Americans' superior arms. However, the Filipinos did have the advantage of knowing their own country and rough terrain well, in contrast to the Americans who were fighting on foreign terrain.

In recognition of United States military service during the Philippine–American War, the United States military created two service decorations which were known as the Philippine Campaign Medal and the Philippine Congressional Medal. In 1916 the United States granted the Philippines self-government and promised eventual independence, which came in 1946.