The remainder of the building dates principally a rebuilding undertaken between c. 1489 and c. 1587, when three successive members of the Molyneux family held the office of rector.

St Helen's is notable for its carved Tudor woodwork, including seven screens which are described in the Buildings of England series as a "gorgeous display" and the "great glory of the church".

The history of the land before this is unknown, but the distinctive oval shape of the churchyard suggests that it may have been used as Saxon burial ground in pre-Conquest Britain.

A small, decorated chapel in the Norman architectural style is known to have existed by 1291,[7] when the building's worth was estimated at £26 19s 4d in the Valor of Pope Nicholas IV.

By 1320, the original building had been completely removed and replaced with a more contemporary Decorated structure, which incorporated a small nave with pointed, geometric tracery windows and pitched roofline.

A west steeple with angle buttresses, a cornice and parapet with beehive-shaped pinnacles[3] and distinctive tall spire was also built adjoining it.

The smaller windows, rough joint with the tower, lack of embattled parapets, and large sections of arch mouldings which make up the North wall all suggest that this was the case.

[citation needed] The oak stalls in the chancel and twenty six rows of pews lining the nave were carved especially for Sefton, and date to around 1590; all have finials in the poppyhead style.

[2] A large, 14th-century muniment chest, four hatchments to the Blundell family and a series of carved wooden pews are located in the north and south chapels.

[citation needed] The octagonal baptismal font which is 15th-century and out of place in the West end of the church, lacks its original painted decoration but has received a plain wooden cover dated 1688.

Oak boards painted in gold leaf displaying the Ten Commandments and Apostles' Creed hang in the tower and date to a similar period.

Those that survive today are the characteristically Georgian austere, dark-wood panelling, complete with a relief pillar design highlighted in gold, which replaced the 17th-century Creed and Commandment boards behind the altar.

Their installation will have prompted the moving of the font from its orthodox standing place at the South door to the rather unconventional site it now occupies in front of the tower.

[citation needed]Following the Victorian Gothic Revival movement of the 1830s, St Helen's was extensively restored during the late 19th and early 20th centuries, taking the appearance of the church back to a pre-Reformation style.

The most significant changes were the removal of the Georgian galleries and whitewashing, but by far the most striking was the addition of the carved wooden ceiling in the nave and side aisles.

[citation needed] An engraving of the interior, showing a bridal couple, in Fisher's Drawing Room Scrap Book, 1834 is accompanied by a skit by Letitia Elizabeth Landon on the folly of marriage.