Heathencote (also called Hevencot in earlier times) was traditionally counted as a manor under the greater manor of Paulerspury, rather than as a hamlet or parish in its own right. As such it is difficult to derive consistent summary statistics which would allow accurate tracking of its population and development until national censuses began in 1841. One survey in the 1520s puts the number of households at about 9.
The manor of Heathencote can be traced back to the latter part of the 12th century. Geoffrey de Lisle was given permission to elect a chaplain to serve in the chapel belonging to the abbey of St James, Northampton. Of this chapel there is little further record and by the 18th century no physical trace at all. The manor passed through the hands of several families: the de Temenels, the de Weedons and the de Paveleys till in the 1360s it was purchased by the Greens of Greens Norton and incorporated with their manor there. Following the death of the last Sir Thomas Green in 1506, the manor passed to his two daughters and their husbands a Vaux and a Parr, and consequently to their respective sons. When they died, the land reverted to the Crown.
Heathencote was made part of the honor of Grafton and passed to the 2nd Duke in 1706, but this was not the whole of Heathencote Manor as had existed in 1506. In 1535, part of the Vaux land had been sold as "a manor or farm" to the Downhalls (also called the Donhaults). In 1725 they sold it to the 1st Earl of Pomfret, who merged it with the rest of the Pomfret Estate holdings in the area. The Heskeths succeeded the Pomfrets.
Heathencote was inclosed along with the rest of the Paulerspury parish in 1819, though records from 1728 show that it had its own fields, named as Follow Field, Peas Field and Wheat Field. The inclosure process rationalised the holdings of the Pomfret and Grafton estates, since exchanges of land holdings also took place. The result of this process was that the Pomfret estate held Park Hall and all land north of Cappenham Bridge Road, while the Grafton estate now held the farm at the eastern end of the village and all the land to the south of the lane to Grafton. Following inclosure, the 4th Duke embarked on an extensive development programme. He rebuilt the farm at Heathencote and the farm at the southern end of Pury End, and established a completely new farmstead on the eastern fringe of the village, a farm which became known as The Hill or Pury Hill Farm. The farms remained part of the Grafton estate until the large-scale estate sales of 1919 and 1920, when they were sold privately before the main auction took place.
The Heathencote area was always mainly agricultural in nature. However, throughout the 18th century there was a brickmaking kiln operating in the village and records from 1757 show that there was also a potash kiln on one of the Grafton estate farms.