Pairin was born in Papar but his hometown is in the interior district of Tambunan, to a retired police officer, Datuk Francis Xavier Kitingan Sobunau (1895–1996) and his second wife, Datin Lucia Laimah Imbayan (1913–2011), natives of the said district who hailed from two villages, namely Karanaan, which was located just behind Tambunan town centre as well as Nambayan, located on the road leading to the main Interior Division town of Keningau.

Pairin is a Catholic, married to Genevieve Lee, a retired teacher of mixed Hakka Chinese (Sino-Native) descent.

However, BERJAYA and the United Sabah National Organisation (USNO) joined forces submit their candidate as the chief minister, but after riots by BN followers, the newly formed coalition between BERJAYA and USNO was dissolved giving PBS the majority government.

He held the post of Sabah Chief Minister from April 1985 to March 1994, during which he spearheaded his party's triumphant outings in four successive state elections (1985, 1986, 1990 and 1994).

[9] On 6 June 2015, Pairin asserted a "clear connection of the incident to the 2015 Sabah earthquake that has brought about so much damage and loss of lives" by a group of European nude tourists on Mount Kinabalu.

However, there is a growing concern that Pairin is no longer suitable to hold the Huguan Siou title and that he should give way to the younger generation.