The Arthur Kill station, which has been planned since the 1990s, will open at 5 a.m. and replaces the current outdated Atlantic and Nassau stations on the line.
"This new station has been a long time coming but it's well worth the wait," said MTA president Veronique Hakim in a statement.
"The new station allows us to move Staten Island transportation another step into the future along with other major projects like the rehabilitation of the St. George Terminal, the recent reopening of the improved Grasmere station, new rail cars and bringing real-time train arrival information to all stations."
The $27.4 million station, on Arthur Kill Road between Lion Street and Barnard Avenue, includes a new 150-space parking lot for commuters, bicycle racks and surveillance cameras.
The new platforms are joined by a pedestrian bridge which will feature 28 glass panels depicting images of wildlife and landscape scenes titled "Tottenville Sun, Tottenville Sky" and designed by Staten Island-native Jenna Lucente.
The MTA also relocated an S78 stop to be in front of the new station and parking lot.
Starting on Saturday, the Atlantic and Nassau stops, which have low ridership and small platforms, will be taken out off SIR service and the city plans to demolish them, the MTA said.
The Arthur Kill station broke ground in 2013 and was originally scheduled to open in 2015, but it was pushed back two-years because of design changes to improve resiliency after Hurricane Sandy, the MTA said.
The station is the first new one for the SIR since the MTA took over the system in 1971.