Hajdina was first mentioned in medieval documents in 1164. In 1202 the settlement had already been split to Spodnja Hajdina belonging to Salzburg, and Zgornja Hajdina belonging to the provincial count and boasting a church and the court. Traces of the latter two can also be found in written documents from the 16th and 17th centuries, but nowadays there are no tracks of them any longer. At the beginning of the 19th century, the borough of Hajdina counted 86 houses and 399 residents; at the end of the same century: 123 houses and 635 residents. In addition, two annual livestock fairs were allowed, on 1st May and 30th August. The residents were mostly engaged in apiculture, agriculture and cattle breeding.
After 1850, once municipalities had been established, the municipality of Hajdina had its headquarters in Zgornja Hajdina, and was independent until 1952 when it became a district in the big Ptuj municipality. Since 1999 Hajdina has been anew an independent municipality. It is composed of seven residential quarters which are all rurally urbanised. The majority of households are not rural. The economy is quite developed. Numerous associations and clubs take care of the social part of life as well as of the preservation and presentation of natural and cultural heritage of the area.