Nearly 300,000 passengers rely on the LIRR daily to travel between New York City, its boroughs and suburban Long Island.
Some 3,500 workers are taking part in the strike, including locomotive engineers, machinists and signalmen.
This is the first time the LIRR rail workers have staged a strike in 32 years.
A group of five unions called their workers to participate in the walkout after negotiations with the Metropolitan Transportation Authority (MTA) ended without a deal.
The LIRR system serves nearly 300,000 passengers per day, connecting New York City and its boroughs with suburban Long Island.
Both sides of the labor dispute said the fight centered on wage increases and health care premiums.
The International Brotherhood of Teamsters union said rail workers have gone three years without raises during the bargaining process.
Kevin Sexton of the National Vice President of the Brotherhood of Locomotive Engineers and Trainmen said no new negotiations are planned between the two sides.
"We're far apart at this point," Sexton said. "We are truly sorry that we are in this situation," he added.
For its part, MTA chairman Janno Lieber said the agency "gave the union everything they said they wanted in terms of pay" and that to him it was apparent the unions always intended to walk out.
MTA said that the union's initial demands would lead to fare increases.
But it would be most troubling for workers if the strike continues into the work week, with New York's already overloaded highways seeing extra traffic.
MTA announced plans to provide a limited number of free shuttle buses during rush hours for essential workers.
New York's Governor Kathy Hochul urged LIRR riders to work from home if they are able to.
Hochul also blamed the strike on union leadership for "unnecessary dysfunction and thousands of union LIRR workers are being forced to go without a paycheck." "I stand with LIRR riders and will fight to preserve the long-term stability of the MTA," she added.
Edited by: Karl Sexton Congestion pricing: Is NYC’s traffic toll paying off?
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