The oldest documentary sources mention this area only at the time of the Christian reconquest of the Iberian peninsula from the Moors, regarding the repopulation of the region after the victory of the forces of Ramiro II de Leão in the battle of Simancas (939). The defense of this part of the territory was entrusted to Rodrigo Tedoniz, husband of Leodegúndia (sister of Mumadona Dias) with whom he generated D. Flâmula (or Chamoa Rodrigues). Rodrigo would become mayor of the castles of the sovereign and, in that role, he would have determined the rebuilding of Penedono Castle. Subsequently, in 998 of the Hispanic Era (960 of the Christian Era), Chamoa Rodrigues, being seriously ill, led himself to the Monastery of Guimarães, instituting his aunt Mumadona as executor, with the burden of disposing of his goods for charity. These included a number of castles and their people (penellas et populaturas) on the border of Beira Alta, including this one, Penela.

During the 11th century, with the advances and retreats of Christian borders, Penedono and his castle changed hands on several occasions. Its final reconquest was due to the action of the Leonese king Fernando Magno (1064). An inventory of the goods of the Guimarães Monastery, drawn up in 1095, lists the Castle of Penedono among other goods previously bequeathed by D. Chamoa. With the political emancipation of Portugal, its domains started to integrate those of the young nation. D. Sancho I (1185-1211), in view of the strategic situation of Penedono, close to the border line, encouraged the repopulation of these lands through Foral (1195), at the same time as it determined the reconstruction of its defenses. His successor, D. Afonso II (1211-1223) confirmed his charter in 1217. The town and its castle also had the attention of D. Dinis (1279-1325), who determined reinforcements in the defense.

The current configuration of the castle dates back to the end of the 14th century, when D. Fernando (1367-1383) included the settlement in the term of Trancoso. Faced with the intention of the city to destroy the Castle of Penedono, the good men of this village rose up, achieving their autonomy. These domains were then donated to D. Vasco Fernandes Coutinho (Marialva), lord of the Couto de Leomil, who had the castle rebuilt.

In the context of the 1383-1385 crisis, having died in the spring of 1384, the mayor of Penedono, Vasco Fernandes Coutinho, succeeded him in the role of his son, Gonçalo Vasques Coutinho. Loyal to the Mestre de Avis party, he was entrusted, at the beginning of 1385, with the task of leading the forces of Porto that conquered Castelo da Feira. Later, he distinguished himself, on merit, in the battle of Trancoso (May 1385), which earned him the promotion to the rank of marshal. It is believed that, in the Castle of Penedono, the sons of this mayor were born and, among them: the firstborn, Vasco Fernandes Coutinho, 1st count of Marialva, who was part of the ill-fated expedition to Tangier (1437); and Álvaro Gonçalves Coutinho, the knight nicknamed Magriço, hero of the narrative of the Twelve Pairs of England, immortalized by Camões in Canto VI of Os Lusíadas.

The descendants of the Count of Marialva maintained interests in the Castle of Penedono, namely: D. Gonçalo Coutinho, who inherited the title of the county, and D. Fernando Coutinho, both members of the second expedition to Tangier (1464), where the first lost his life ; his grandchildren, D. João Coutinho, 3rd count of Marialva, and D. Francisco Coutinho, 4th count of Marialva by the succession of his brother, deceased without descendants, both members of the expedition that conquered Arzila (1471), who at the first cost life.

Under the reign of D. Manuel I (1495-1521), the town received the Foral Novo (1512), which attests to its importance at the time. At this juncture, new works were carried out at the castle, to which the influence of the 4th count of Marialva, the winner of the royal works in Beira, contributed, whose only daughter, D. Guiomar Coutinho, married the infant D. Fernando. The Count died without descendants, and his daughter, two years later, also without descendants, the Coutinho family was extinguished.