Repairs to the Jeffrey Street church were funded by worshippers' collections and grants from Historic Scotland and the Heritage Lottery Fund.
Work on the building included extensive repairs to the roof and the replacement of some extremely weather-worn masonry.
Canon Ian Paton, the Rector, said: "I'm delighted the work has been completed successfully and the scaffolding has come down in time for Easter, which is the most joyful Christian festival of all.
"It's important to us that our newly refurbished Crucifix can now be seen by everyone, because the new life that it stands for is for everyone as well."
The congregation of Old St Paul's, hidden away off the High Street, can trace its history back to 1689 when Bishop Rose, unwilling to renounce his oath of allegiance to King James Vll and II, had to leave St Giles Cathedral.
He first set up a congregation in a wool store in Carrubbers Close as one of the earliest congregations of the Scottish Episcopal Church. The present church was begun, on Jeffrey Street, in 1883, ten years after the unsafe old wool store was demolished.
The building has been steadily maintained over the years but time had taken its toll. Contractors Campbell & Smith of Ormiston worked on the pointing and replacement of masonry, renewal of lead and the guttering.
The congregation have so far raised more than 29,000 and the Heritage Lottery Fund and Historic Scotland each contributed 89,500. Fundraising will go on.
Additional grants were awarded by the Scottish Episcopal Church (15,000) and Scottish Churches Architectural Trust (5,000).
Culture Minister Fiona Hyslop said: "The congregation of Old St Paul's, like so many of Edinburgh's workers, will be very glad to see the scaffolding gone and the church revealed again."
Colin McLean, Head of the Heritage Lottery Fund in Scotland, said: "I am so pleased that this gem of a church is now in a good state of repair and congratulate the congregation for making that happen. With scaffolding gone, the entrance to the church is once more a feature of Jeffrey Street and I would encourage people to step inside and experience the magical 'Tardis' effect of Old St Paul's."
The repair project was directed by John Sanders, a specialist in the conservation of buildings, and a partner in Simpson & Brown, Architects. He said: "Simpson & Brown are delighted to be working at Old St Paul's Church. It has one of the best 19th-century church interiors in Britain."