Kimberly was promoted to captain on October 3, 1874, and commanded the sloop on the South Atlantic Station in 1875–76, and the screw sloop in the Pacific in 1877–78. During the early 1880s Kimberly served at the New York Navy Yard, and was the President of the Examining and Retiring Board in 1883–85, gaining promotion to commodore on September 27, 1884. He was appointed Commandant of the Boston Navy Yard in 1885, and attained the rank of rear admiral on January 26, 1887. He was then appointed the Commander-in-Chief of the Pacific Squadron. In March 1889, during the Samoan crisis, his flagship was struck by a violent cyclone while at harbor at Apia. Guiding his men with the words, "If we go down, let us do so with our flag flying," Kimberly skillfully beached his flagship, losing only one man in the raging storm that wrecked "Trenton". Following his return to the United States in January 1890, Kimberly was appointed President of the Board of Inspection and Survey; holding the post until his retirement on April 2, 1892.