In the late nineteenth century, British colonial authorities found the church in need of rebuilding, in light of its importance. They demolished it in 1893 and planned for it to be rebuilt in a neo-Gothic style — a revival of medieval architectural idioms that was popular in Europe, especially in England, in the nineteenth century. The present structure shows key features of Gothic cathedral architecture — an emphasis on vertical elements in the form of pointed arches, pinnacles and tall spires; profuse decoration through facade detailing, tracery and stained glass windows; and rib-vaulted ceilings. 

The church is built on a cruciform floor plan in the form of the Latin cross typical of medieval European church architecture, with an area of about 780 square metres. The two-storeyed, whitewashed structure is dominated by a 47 m tall spire, which abuts the west-facing entrance — at the long end of the cross — and serves as the bell tower. A smaller spire is built over the transept, where the two axes of the cross plan intersect; this spire originally marked the location of the saint’s tomb. Both spires are of octagonal sections, tapering to a tall point. 

The front facade features six pointed arches — three doorways and three nearly identical windows above — and a pediment, flanked by two octagonal towers topped by belfries and small spires mimicking the larger spires. These pointed arches are seen along the entire structure, in arcades at the ground level and windows at the upper storey. A series of pinnacles runs along the top perimeter of the church. Other elements of Gothic architecture such as stringcourses are seen on the exterior, as well as numerous mouldings of the trefoil motif and the trefoil cross. A pitched roof covered in Mangalore tiles shelters all four arms of the building. 

The long arm of the cruciform constitutes the main hall or nave, which features a fan-vaulted teak wood ceiling. A row of arched doorways along both sides opens onto arcaded verandahs, which are roofed at the first-storey level in Madras terrace. Above them is a row of clerestory windows set with stained glass. Behind the altar, a stained-glass window set in a pointed arch — instead of the typical circular rose window — depicts the popular story of Doubting Thomas, in which Thomas is seen touching the side wound of Jesus Christ. The stained glass panels of the church were commissioned from the historic studio Mayer & Company in Munich, Germany. The wooden statue of Jesus against the Holy Cross at the altar shows his feet resting upon a lotus and flanked by peacocks. A pipe organ added to the cathedral by the British in the nineteenth century is housed in the narthex. 

The church was first renovated in 1952. In 2004, church authorities began restoring and remodelling several parts of the building’s interiors, especially the floor, ceiling, stained-glass windows and the tomb, though the exterior retains its nineteenth-century appearance. The floor was re-laid in marble; the paint on the ceiling was removed to expose the original finish of the wood. Other changes to the cathedral included the installation of an ornate wooden altar for the Our Lady of Mylapore statue. The tomb of the saint, previously in an open crypt built into the floor of the transept in front of the altar, was shifted to an underground chapel in a new building that serves as the information centre and also houses a museum and auditorium. In addition the church complex today includes two chapels, several administrative offices, the head priest’s residence, and a liturgical centre — largely recent structures, built or renovated in 2004. 

The museum contains the head of a spear believed to have killed Thomas, discovered during Portuguese excavations in the sixteenth century. Other important relics on the site include what is known as the Thomas pole — a wooden pole believed to have been fashioned by Thomas to protect the land and its dwellers from the sea. A popular belief holds that this pole prevented the destruction of the cathedral and its neighbouring areas during the tsunami that hit Chennai in 2004.

The church is a major religious site in Chennai, regularly used and well maintained. It hosts an annual ten-day festival in June–July for the Feast of Saint Thomas, which celebrates the death anniversary of the saint: a statue of Thomas is paraded on a golden chariot in processions along Santhome High Road, in the vicinity of the church.