Previously, the project has faced years of delays. Erdogan plans to head for Istanbul in the first train Friday evening.
The railway inauguration also comes ahead of presidential elections next week on August 10, and Erdogan promised constantly during his campaign that he would improve the nation's infrastructure.
Much of Turkey's current railway system was planned and built by foreign countries in the era of the Ottoman Empire, while high speed trains have already been running since 2009 between the capital city and Eskisehir.
However, weeks before the inauguration, a train crash occurred on the Ankara-Istanbul high speed rail track when a testing was being conducted.
The test train partially derailed after it collided with a maintenance vehicle around the town of Gebze in a Turkish province to the east of Istanbul, raising safety concerns in a country that sees frequent railway accidents. In July 2004, dozens of people were killed when a high-speed train derailed in the northwest.
The new railway express will shorten the journey time between the two metropolises to three hours and a half, Turkish Transport Minister Lutfi Elvan told reporters, adding that this railway is capable of reaching a speed as high as 250 km per hour.
The Ankara-Istanbul line has cost the Turkish government some 4. 25 billion U.S. dollars, and is expected to change the travelling habits of the Turkish countrymen, a vast majority of whom make their long-distance trips by bus or plane. Endi