The work has already begun and starting Friday evening, bulldozers will replace trains at the intersection of Duboce and Church.
"To shut down the busiest rail line and to cause great diversions for other lines will certainly have an impact on a lot of people," said Edward Reiskin from the SFMTA.
The N-Judah runs the entire breadth of the city from Ocean Beach to Caltrain, serving at least 20,000 riders on weekdays.
It will shut down completely tomorrow at 7 p.m. and not reopen until nine days later, June 4 at 5 a.m.
There will be partial shut-down of the J-Church. The 22 Fillmore and N Owl will be re-routed. The service disruption is to allow for a complete overhaul of the rail system and roadway along Duboce and Church. These MTA renderings show improvements for pedestrians, bikes and cars.
"I'm going to have to look for alternative bus routes or walk," said Muni rider Chris Macolino.
"I'll have to take the 71 or the 43 or the 22. You can take the ones up on Parnassus. It's an inconvenience, won't be fast like this but has to be done," Muni rider Nick Armatas.
There are a variety of bus alternatives and the MTA has a special plan in place for the Golden Gate Bridge anniversary event Sunday, where 300,000 are expected to attend.