During the Middle Ages, Palenciana was part of Benamejí. During the Muslim era it belonged to the Cora de Rayya (Málaga) and, after the fall of the Caliphate, to the Kingdom of the Banu Ziri of Granada, despite its having been initially incorporated by Fernando III into the Christian domain. It was laterdonated by Alfonso X to the Military Order of Santiago and was within the border of Granada, so was affected by the numerous military and civic changes in the city until it conquered Antequera in 1410.
Throughout these many ownerships, Palenciana remained indissolubly united to Benamejí; it is only since the sixteenth century that the village has existed as its own entity. As a result of the real resolution to dismember Benamejí's donation from the Military Order of Santiago, in 1547Juan de León was sent to the area to carry out an evaluation of the term that would allow the compensation to be paid.
In 1547 the current town was not yet built, although some sources mention a 'cortijo' in the Palenciana area,possibly located on the site of the current municipality. It was after Diego de Bernuy purchased the Señorío of Benamejí that houses were built around the primitive farmhouse, following the model of Benamejí.
Palenciana achieved segregation from Benamejí in 1834, ending the dependency and forming its own town hall and administration.