He married three times.
With his first wife Kukakina, he had a son named William F. Kaʻae (1870–1938), who became a county official for the Territory of Hawaii.
His second wife was Kamehaokalani, a relative of Queen Kapiʻolani, and they had three children.
His third wife Jessie Kapaihi Lane, sister of Honolulu Mayor John C. Lane, survived him.

In later life, Kaʻae attempted to claim, on behalf of his deceased second wife, the lands of Kealiʻiahonui, the son of the last independent king of Kauai Kaumualiʻi.
His suit stating that the last will of Kealiʻiahonui was forged was rejected by the courts.
In 1893, almost immediately following the overthrow of the Kingdom of Hawaii, the Kaae petition was accepted and the probate of Kealiʻiahonui was reversed by the provisional government as the first case heard by Dole after the overthrow.

Kaʻae died of blood poisoning at Queen's Hospital in Honolulu.
His funeral was held at the Cathedral Basilica of Our Lady of Peace and he was buried at the Kawaiahaʻo Church cemetery.
He married three times. With his first wife Kukakina, he had a son named William F. Kaʻae (1870–1938), who became a county official for the Territory of Hawaii. His second wife was Kamehaokalani, a relative of Queen Kapiʻolani, and they had three children. His third wife Jessie Kapaihi Lane, sister of Honolulu Mayor John C. Lane, survived him.
In later life, Kaʻae attempted to claim, on behalf of his deceased second wife, the lands of Kealiʻiahonui, the son of the last independent king of Kauai Kaumualiʻi. His suit stating that the last will of Kealiʻiahonui was forged was rejected by the courts. In 1893, almost immediately following the overthrow of the Kingdom of Hawaii, the Kaae petition was accepted and the probate of Kealiʻiahonui was reversed by the provisional government as the first case heard by Dole after the overthrow.
Kaʻae died of blood poisoning at Queen's Hospital in Honolulu. His funeral was held at the Cathedral Basilica of Our Lady of Peace and he was buried at the Kawaiahaʻo Church cemetery.
Junius Kaʻae