Pakenham Mill was built in 1831. Clement Goodrich was the miller in 1846, when he took on an apprentice. The Pakenham Mill came into the ownership of the Bryant family in 1885. A steam engine was used as auxiliary power. In 1947, the mill was nearly tail-winded, but the miller managed to turn the cap in time to avoid this happening. Pakenham Mill was restored in 1950, with a new weatherbeam fitted by Amos Clarke, the Ipswich millwright. At this time the swing-pot neck bearing from Buxhall mill was installed. A second-hand stock from Thurston post mill was fitted at this time and a gallery constructed around the cap. The gallery was based on that at Wendover mill, Buckinghamshire. New sails were also fitted.

Further restoration on Pakenham Mill took place in 1961, aided by grants from Suffolk County Council, the Ministry of Works. The work was conditional on the Bryant family continuing to work the mill. The restoration work was carried out by R Thompson & Sons Ltd, millwrights of Alford, Lincolnshire. The copper covered cap was rebuilt and clad in aluminium for maintenance reasons. A new stock and two new sails were made, and the fantail rebuilt. Pakenham Mill was struck by lightning in June 1971, a stock being split and a sail damaged. The sack chain saved the mill from being burnt down by giving a route for the lightning to earth. When the mill was repaired, a lightning conductor was added to the mill.

The most recent restoration of Pakenham windmill was completed in May 2000. The £60,000 cost of the work was 80% funded by the Heritage Lottery Fund. The work was carried out by Thompson's of Alford.