At a Vestry meeting on Monday 30th March 1891, the Rev. H. Sidall had informed those present that he intended to rebuild St. Thomas's Church. It was proposed to rebuild the Church of stone, and it was supposed that a good deal of the stone on the present building would be available, but it would cost something to dress it and trim off the bad parts. As the vicar understood it, the architects and builders were unable to form an estimate of what a Church under those conditions would cost. The plan, however, had been submitted to a Manchester builder, and he fixed the cost at £5,275. That was for a new building altogether, and not allowing for old material. With regards to funds, the Vicar informed the meeting that they had a little over £1,000 in the Court Chancery, and this would be handed over to them as soon as they commenced operations.

There was a further legacy from Mr Samuel Stock of Blackley Hurst. The amount mentioned in Mr Stocks will was £9,000, which was in certain colliery shares in the neighbourhood, but these had depreciated so much that the amount that could be obtained from them was little over £1,000. This was a great disappointment, for the Ashton people had long been looking forward to the prospect of a new church. The Vicar said that the architect would have to reduce the cost to £5,000 and they would then have to raise £3,000. He trusted the landowners in the township would give them material help, and he also expected to receive considerable outside support. An appeal for funds was made in April 1891, and in the event, within two months subscriptions were promised to cover the whole cost. The architect selected to rebuild the Church was Mr F. H. Oldaham of John Dalton Street Manchester. The work was carried out by Mr Wm. Winnard, contractors of Wigan, and Messers France & Smith Joiners and builders of Pemberton. The original tender for the work was £4,750 but certain extras.

The last services were held in the old Church on Sunday 26th July and the following day demolition of the building was commenced. It took about four months to take down the old Church and to clear away the rubbish, and it was not until December 5th 1891 that the foundation stone of the new Church could be laid. This was done by Colonel W.T. Leigh of Lyme Park, Cheshire (afterwards Lord Newton). Beneath this stone there was placed by Lady Gerard a sealed jar containing a copy of the Liverpool courier of the day, copies of the Parish Magazine with a list of subscribers to the Church building fund, a copy of the service used on the occasion, Silver and Copper Coins of the year 1891, and a document stating that the jar had been played by the Right Hon. The Lady Gerard of Garswood. The stone was thought to be on the South side of the Chancel Arch near to the lectern, but there was no inscription and there is nothing now to tell which it is.

Whilst the work of rebuilding was going on, the services were at first held in the large classroom, but this was found so very inconvenient that the building committee decided to buy an Iron Church, and the tender Mr. Lee of Manchester for one to cost £400 and to seat about 400 people was accepted. This was erected on a plot of land just outside the Churchyard and answered its purpose fairly well, although it was not nearly large enough to hold the congregation from the old Church, which would accommodate 800 and was generally well filled. This Iron Church, when its purpose was served was afterwards removed to Stubshaw Cross where it was known as the mission of St. Luke.

The new Church took eighteen months to build. It was completed in 1893 and had seating accommodation for about 500 persons, 300 less than could be accommodated in the old Church with its galleries. It was 109 feet long and 61 feet wide, with a nave of 23 feet in width, and North and South aisles each 19 feet wide. The chancel was the same width and height as the nave.

In the rebuilding, as much as possible of the old Church was made use of, and the new stone was selected of the same kind- Runcorn red sandstone. In erection, care was taken to mix the old weather beaten stones with the new, so as to emphasise the fact that it was not an entirely new Church but a restoration. This result was certainly achieved as the Church can be taken for a much older building than it is. The Tower which was purposely kept low was built to hold a peal of bells, but at first only the bell which came out of the small bell turret on the old Church was installed. This bell was inscribed "PACK AND CHAPMAN of LONDON, facet 1773" Other fittings taken from the old Church were the clock, dated May 15th 1812 and Organ installed in 1826.

There was a small side chapel on the north side of the chancel, in which all the mural tablets from the old church were placed. Opposite to this was the organ chamber which adjoined a roomy vestry about 20 feet square. In this vestry was placed the old Parish chest of 1669, a fine carved bookcase in very dark oak and the old communion table with its marble top. In the chancel the choir stalls were intended for sixteen men and eighteen boys. The chancel and altar steps were all of oak, the chancel floor being of oak blocks, while all the passages in the Church were of pitchpine block, which was warmer than stone or tiles and had the advantage of being almost silent to walk on. The windows were of a simple tracery pattern, fitted with lead lights.

The Church had many requirements for the future, but as the vicar pointed out St Thomas's was entirely a working class parish and trade was in a very depressed state, so patience had to be exercised. Among the things the vicar wanted to see was a new pulpit, a peal of bells, oak panelling in the Chancel and wood panelling all round to the height of the pews. But the completing of his last undertaking -the beautifying of the Church he built and the panelling of the Chancel- the vicar was not to see.

On Thursday 6th July 1893 the new church was consecrated by the Lord Bishop of Liverpool, Dr. J. C. Ryle. The ceremony of consecration was fixed for 3.o'clock. To mark the event, the scholars of the Parish schools walked in procession through the main streets of the township, led by the St Thomas' brass band. They were joined by the scholars of St Luke’s and the combined procession then returned to the church in time for the ceremony. We learn from eye witnesses that "several banners and bannerettes were conspicuous in the procession, whilst in the vicinity of the church, garlands of varied-coloured streamers stretched across the road."

The clergy present at the ceremony were the Rt. Rev J. C. Ryle, archdeacon Taylor, Rev H. Siddall (vicar of St Thomas'), J. Hurley (Curate), W. J. Melville (Rector of Downall Green), Canon Fergie (Ince), E. A. Dury (St Catherine’s Wigan), Richardson (Golbourne), Carson (Wargrave), Carleton (Warrington), Pigott (Warrington), Berridge (Lowton St Mary’s), Phillips, Smith, Gibbin (a former curate of St Thomas'), Williams and Johnstone.

Having received the petition from the incumbent and Churchwardens, asking him to consecrate the new church, the Bishop signified his assent. Walking in procession from the Altar to the West end of the church and backwards the prescribed consecration was gone through. The Chancellor of the Diocese read the deed of consecration, after which followed the usual service at evening prayer. The lessons read were from 1 Kings Ch.8, v22-30, and Hebrews 10v19-25,. The old Hundredth Psalm-"All people that on Earth do dwell" and the "Churches one Foundation" were the hymns sung, and at the conclusion of the Consecration service the Bishop preached a sermon based on the text "o come let us worship" from psalm 95, verse 6. He drew attention to the fact that the book of Psalms was perhaps the best known book in the Bible. He dealt with the subject of worship in different lights and defined the word as meaning united prayer and praise, which he said was requisite for spiritual life. During the service the choir sang an Anthem, and an offertory was taken on behalf of the building fund.