The A41 is on the line of the Roman road known as Akeman Street that ran from London to Cirencester, which passes through this parish. Roman pottery was found during fieldwalking south of Collett Farm.
A Saxon burial with brooches inlaid with garnets was found in a quarry near Hill Cottages in 1848. This probably dated to the Early Saxon period, perhaps the 7th or 8th century. By the 9th century (AD 845) the parish boundary with Brill had been established and seems to have followed the edge of Rushbeds Wood, where a ditch can still be seen. A trackway on the parish boundary near Clearfield Cottages may also date back to the Saxon or medieval period.
Wotton Underwood is recorded in Domesday and was part of Bernwood Forest from before that time. Bernwood had been a hunting forest from the time of Edward the Confessor. It grew to its largest extent under Henry II. The whole area was not covered by woods; in the medieval period a forest was a place where deer roamed for hunting and so included open land, villages and fields. All those who lived in the forest were not allowed to hunt or even gather wood without a special licence from the king. Bernwood Forest was finally disafforested in the reign of James I in 1635, although it had been shrinking in size since the time of King John (1199-1216).
Ridge-and-furrow, the remains of the medieval farming technique, can be found around Wotton Underwood parish. It was thought that there may have been a medieval settlement that was later deserted in the area of Tittershall Wood, but no remains can be seen there today. It is possible that this was a mix-up with the deserted medieval village earthworks at Tetchwick. The medieval village that was cleared away in the grounds and to the north of Wotton House also has a moat, which may have been the site of a manor house, and a windmill mound. Another windmill, mentioned in a document of 1580, seems to have stood south of Manor Farm along the line of the former tramway.
Many of the listed buildings in Wotton Underwood date to the 17th century. One 17th century document records a vicarage near the churchyard but the current house is 19th century in date, presumably it replaced the earlier building. All Saints' church is the oldest building in the parish and dates back to the 14th century, although a reused 12th century lintel over a doorway into the nave suggests there was an earlier building on the site. Nugent Cottage is the second oldest, being a 15th century cruck-built house with many later alterations.
There were two manors in Wotton Underwood in the medieval period. The main Wotton one and Ham or Ham-cum-Wotton. Ham later joined with Easington Manor. Moat Farm, up near Tetchwick Brook, may have been Ham Hall but the current buildings only date back to the 17th century. Wotton House is on the site of the old Wotton manor house. It was rebuilt in the early 18th century for Richard Grenville but it was damaged by fire in 1820 and so was again rebuilt. The Clock pavilion in the grounds was built at around the same time, in 1704-14, and was not damaged by fire. It is now a separate house, as are other buildings such as the coach-house and laundry. It had interesting 18th century landscape gardens attributed to George London but Capability Brown was also employed in 1739-40 and is thought to have used projective geometry to lay out the gardens. The village of Wotton Underwood was also cleared away for these gardens. There are also many garden buildings in the grounds. The lake in the gardens was used for boating and staging mock sea battles in the 18th century as well. Another watery feature, the duck decoys, were constructed in the 19th century near Sawmill Cottages. They was used for luring ducks into traps.
Also near Sawmill Cottages was a sawmill in the 19th century, just a small part of the general industrialisation of the country. A brick and tileworks belonging to a Mr Foot seems to have been along Kingswood Lane, south of Tittershall Wood. There are also records of a 19th century brick and lime kiln on Brick Hill. Transport was also a major feature of the 19th century and the Duke of Buckingham decided to build a tramway from Quainton to Wotton in 1870. Two years later it was extended to Brill and it was closed in 1935. It's course has been identified in Rushbed Woods. A railway was built by the Great Central company between Grendon and Woodham and the remains of this passes through the parish as well. Some bridges survive along the route. Wotton Station has been turned into houses and so survives in a slightly altered form.
One of the latest changes to the parish was Westcott airfield, which intrudes a little into Wotton Underwood. Westcott airfield was one of the first to have aeroplane simulator training. Before high-tech computer generated simulators, the “Dummy Fuselage Scheme” was put together to train airmen. The fuselage of a Wellington plane was installed in Westcott in September 1942. The pilot sat at the controls and the bomb aimer below him would give instructions for bombing a target projected onto a screen below. Part of Wotton Underwood Park seems to have been used as a military camp during the war as the remains of the buildings can be seen on a vertical aerial photograph from 1947 and can still be seen on the ground. It is thought that Canadians were billeted there, perhaps in the run-up to D-Day.