Soon after this the Colonel, Lieutenant, Colonel and Major of the "Famous Sixth Massachusetts Volunteers" resigned, leaving the regiment in chaos and caused great distress in the old bay state. Lt. Colonel Rice was recommended by General Miles and was soon commissioned as Colonel. This caused great excitement in Massachusetts and the Sixth Mass. Volunteers soon became one of the best regiments in the Army and saw active service in both Puerto Rico and Cuba.

In July of 1898, Colonel Rice was appointed by President McKinley to be the senior colonel of all U.S. Volunteers in the Philippines. He commanded the 26th U.S. Infantry, a New England regiment and he and his troops were involved in many skirmishes against the insurgents and Moros. He also established free schools, took the census, and
administered the oath ofallegiance to over 60,000 natives while he served as the Military Governor of the Island of Panay.

He returned to the United States in July of 1901 after suffering from fever and heart disease brought on by the harsh jungle climate. The Philippine Insurrections was Rice's last war.