Pepin was elected king upon his father's death by the nobles of Aquitaine who were keen to establish their independence from the Empire. However, Louis the Pious had appointed his son Charles the Bald as King of Aquitaine in 832 when he (nominally) dispossessed Pepin I. Pepin had thereafter been at war with his uncle Charles. Louis the Pious fully disinherited him at Crémieux and then at Worms in two subsequent divisions of the empire.
Louis demanded that the Aquitainians send Pepin to Aachen to learn the ways of good governance however they refused. Pepin was in total control of Aquitaine until 841 when he went to his uncle Lothair I's aid at the Battle of Fontenay. Pepin's contingent faced the troops of Charles the Bald and defeated him. However elswhere on the battlefield Lothair was routed by the forces of Louis the German, another uncle. Pepin returned to Aquitaine and continued war with Charles the Bald.
In 844 Pepin made the fatal error of asking the Viking Adventurer Jarl Oscar for military assistance. He guided the Viking force up the Garonne to Toulouse, giving them an opportunity to scout the land for plundering. In 845 Pepin welcomed Seguin of Bordeaux who had defected from the Emperors side and made him dux Wasconum, to help his fight against Sans II Sancion, leader of the Gascons.
In 847 Oscar was given control of Bordeaux, the largest city in Aquitaine and then controlled by Charles, by disaffected citizens: either Jews or partisans of Pepin. This loss of the City to a heathen pirate, coupled with Pepin's penchant for the bottle and loose living, eroded his support in the nobility until 848 he was left with no support. His brother, Charles then left Aachen to claim the Aquitainian Kingdom for himself.
Pepin II's rule finally ended in 851 or 852 when he was captured by Sans II Sancion, who had been at war with his father Pepin I, and handed over to Charles. He was detained in the monastery of Saint Médard in Soissons. As reward Sans was awarded the status of Duke.
However Pepin escaped and recovered some of his old authority and lands in 854. The Vikings now established in the Loire Valley ravaged Poitiers, Angoulême, Périgueux, Limoges, Clermont, and Bourges while Charles the Bald was busy trying to subdue Pepin. In 864 Pepin joined the Vikings and is rumoured to have turned from Christianity to worship Woden and "lived like one of them [the Vikings]". He took part with the Vikings on an attack on Toulouse. He was captured again later in 864 and deposed by the Edict of Pistres, and imprisoned in Senlis, where he eventually died.
Pepin had no known children.