Between the nave and the north and south aisles are two arcades each of four doubly-chamfered arches, supported by circular columns with octagonal capitals.
The chancel floor is three steps above that of the nave.
 It contains choir stalls designed by the architect William Swinden Barber on either side, and in a 1905–1908 chancel reordering these were augmented by two clergy seats and two prayer desks for the choir.
The original choir stalls were described in 1880 as being "plain but very solid construction", like the nave pews which were also designed by the architect.
On the south side of the chancel is the organ chamber, and on the north side is the vestry which has access through the north wall and into the chancel.
The chancel arch was built "as lofty as possible", being the "chief internal feature of the structure".
All the woodwork is made of pitch pine, and was originally treated or varnished to appear as close as possible to its natural colour, although the roof timbers looked warmer than the pews when new.
The nave is 56.5 feet (17.2 m) by 20.75 feet (6.32 m), and the north and south aisles are 56.5 feet (17.2 m) by 9.66 feet (2.94 m).
The chancel is 31.25 feet (9.53 m) by 19 feet (5.8 m).
The organ chamber contained no organ at first, when it measured internally 16.5 feet (5.0 m) by 10.5 feet (3.2 m).
At the consecration, a harmonium was used in default of the absent organ, and the church still contains a harmonium which may date back to 1880.

The font and pulpit, designed by the architect and sculpted by Charles Mawer of Leeds, are made of Caen stone, and were paid for by Lady Ingilby.
The nave and chancel originally had plain brass gas lamp standards made by Hardman's Works, and there was hot-air heating apparatus supplied by Grundy.
The books were given by Mrs and the Misses Lloyd of Hazelcroft.
Plate used for communion service was given by Mrs W. Strother, and the chairs in the chancel were given by Mr H. Cautley.
The surplices and linen were given by the vicar of Killinghall Reverend R.K. Smith and his wife.
Thomas Strother presented the altar in memory of his mother who died in 1863.
Dinah Cautley (d.1910) paid for the oak chancel screen in 1905.

 Media related to Interior of Church of St Thomas the Apostle, Killinghall at Wikimedia Commons 
 Media related to Charles Mawer sculpture in St Thomas the Apostle, Killinghall at Wikimedia Commons
Between the nave and the north and south aisles are two arcades each of four doubly-chamfered arches, supported by circular columns with octagonal capitals. The chancel floor is three steps above that of the nave.  It contains choir stalls designed by the architect William Swinden Barber on either side, and in a 1905–1908 chancel reordering these were augmented by two clergy seats and two prayer desks for the choir. The original choir stalls were described in 1880 as being "plain but very solid construction", like the nave pews which were also designed by the architect. On the south side of the chancel is the organ chamber, and on the north side is the vestry which has access through the north wall and into the chancel. The chancel arch was built "as lofty as possible", being the "chief internal feature of the structure". All the woodwork is made of pitch pine, and was originally treated or varnished to appear as close as possible to its natural colour, although the roof timbers looked warmer than the pews when new. The nave is 56.5 feet (17.2 m) by 20.75 feet (6.32 m), and the north and south aisles are 56.5 feet (17.2 m) by 9.66 feet (2.94 m). The chancel is 31.25 feet (9.53 m) by 19 feet (5.8 m). The organ chamber contained no organ at first, when it measured internally 16.5 feet (5.0 m) by 10.5 feet (3.2 m). At the consecration, a harmonium was used in default of the absent organ, and the church still contains a harmonium which may date back to 1880.
The font and pulpit, designed by the architect and sculpted by Charles Mawer of Leeds, are made of Caen stone, and were paid for by Lady Ingilby. The nave and chancel originally had plain brass gas lamp standards made by Hardman's Works, and there was hot-air heating apparatus supplied by Grundy. The books were given by Mrs and the Misses Lloyd of Hazelcroft. Plate used for communion service was given by Mrs W. Strother, and the chairs in the chancel were given by Mr H. Cautley. The surplices and linen were given by the vicar of Killinghall Reverend R.K. Smith and his wife. Thomas Strother presented the altar in memory of his mother who died in 1863. Dinah Cautley (d.1910) paid for the oak chancel screen in 1905.
 Media related to Interior of Church of St Thomas the Apostle, Killinghall at Wikimedia Commons 
 Media related to Charles Mawer sculpture in St Thomas the Apostle, Killinghall at Wikimedia Commons
Church of St Thomas the Apostle, Killinghall