Deep inside a subway station in Brooklyn, in a cramped, industrial room, Dyanesha Pryor pushes in a metal lever on a hulking machine that was installed nearly a century ago. A few hundred feet away, a signal light flashes red and a train that had been rumbling down the local tracks slides to a stop.

Ms. Pryor, a transit worker, pulls another lever and a section of rail shifts into place, allowing the local train to merge onto a shared track in front of a waiting express train. She then restores the signal to green and the local rolls into the station.

Ms. Pryor repeats this sequence — punctuated by the clank, clank, clank of the levers slamming into place — dozens of times over the course of the day in the hidden control room at the Hoyt-Schermerhorn station.

Thousands of subway riders a day depend on Ms. Pryor for a smooth commute. But if she has to unexpectedly step away, even for a bathroom break, all express service is rerouted to the local tracks until she returns. “Everybody has to go local because there’s nobody here to move the levers,” said Ms. Pryor, 35.

About 85 percent of New York City’s subway system still operates with this analog signal system. The outdated equipment is no longer manufactured and has to be manually operated, around the clock.

It’s no surprise then that the system is a leading cause of delays. Over the past 15 months, it has led to average of nearly 4,000 train delays a month, according to data from the Metropolitan Transportation Authority, the state agency that runs the city’s transit system.

The subway has long depended on “fixed block” signaling, a method of maintaining safe distances between trains that uses track circuits to detect the location of trains, wayside signals similar to traffic lights and mechanical trips to stop trains that pass a red light.

The authority is replacing the system with a modern upgrade known as communications-based train control, or C.B.T.C., which is becoming the standard for transit systems worldwide, including those in London and Paris. It relies on computers and wireless technology — instead of people — to automatically control train movements.

But the system upgrade is at risk. The Trump administration is attempting to kill congestion pricing, a tolling program in Manhattan that would raise billions of dollars for the work. The M.T.A.’s next capital budget could also be in jeopardy, if Washington follows through on its threats to defund transit projects in New York State.

Ancient Signals

New York’s subway is vastly more complicated to run than other major subway systems because it never closes and its trains crisscross tracks. The city’s subway has more than 200 crossing points known as “interlockings.”

Much of the old signal system is run from a network of underground control towers that sit beside the tracks. Inside each tower are operators like Ms. Pryor who change signals and switches.

About 300 operators like Ms. Pryor are stationed at interlocking machines, but their ranks are thinning as the subway has gradually moved to centralized controls. The work pays around $40 an hour on average, according to a Transport Workers Union wage sheet.

While the signaling system still works most of the time, it has become more fragile and unreliable with every passing year. Equipment and parts break or wear out. In January, a relay failure at the Hoyt-Schermerhorn station took about an hour to fix and delayed 25 trains.

“If you had a car from the 1930s and drove it every day you’d be lucky if it was still working like this, right?” said Salvatore Ambrosino, the M.T.A.’s chief officer for signals.

Fixed block signaling divides the tracks into blocks, or sections of roughly 1,000 feet on average, that carry an electrical current. When a train occupies a block, it cuts off the current, letting the system know its general position.

The system cannot pinpoint exactly where a train is, so a buffer of two or more blocks is maintained between every train to keep them at safe distances. But that limits how many trains can run at the same time. As subway ridership has grown, it has resulted in overcrowded cars and longer waits.

Modern Signals

The old signals are gradually being replaced with C.B.T.C., which keeps trains in constant contact with a centralized computer system that controls their every movement. This technology allows trains to run closer together, which means more trains on the tracks and faster service.

“Think of it like moving from a Walkman with all the moving parts to an iPhone that’s solid state,” said Jamie Torres-Springer, president of M.T.A. Construction & Development, which is overseeing the signal projects. “There’s no moving mechanical equipment — it’s all digital.”

In 2006, the L line became the first route to convert to the more modern system. The 7 line followed in 2018. Those routes now consistently have the best on-time performance.

C.B.T.C. has also been installed on sections of the E, F, M and R lines in Queens and the F line in Brooklyn.

The advantage of the new system is that computerized equipment is installed on every train to monitor its exact location and speed. The computers digitally manage signals and switches while routing the trains.

Mission Control

The home of C.B.T.C. is the M.T.A.’s Operations Control Center in Midtown Manhattan. Security is extremely tight and photos are rarely permitted.

Entering the control center is like walking onto the bridge of a spaceship. The nearly 21,000-square-foot room is almost half an acre in size with soaring 30-foot high ceilings. An entire wall is covered by a digital map showing trains moving in real time in Brooklyn, Manhattan and Queens.

Between 75 and 90 M.T.A. workers are on the floor, day or night, surrounded by 432 computer screens. They keep an eye on train movements, stepping in only to troubleshoot. Each time another route is converted to C.B.T.C., more workers join them.

The next round of projects will bring modern signals to 66 miles of track in Brooklyn and Manhattan. These tracks are shared by six different routes — the A, C, B, D, F and M lines — and carry about 1.6 million daily riders.

C.B.T.C. will eventually be expanded to subway routes across Manhattan, Brooklyn, Queens and the Bronx.

But modernizing the signals, which have been called the subway’s central nervous system, is enormously expensive. While the transit authority has brought down costs significantly as the scale of work has increased, installing C.B.T.C. costs about $25 million per mile. The work also includes overhauling tracks and infrastructure and retrofitting trains.

M.T.A. officials are counting on $3 billion from New York’s congestion pricing program to pay for the new signaling system. But that funding is in question now that President Trump has vowed to kill the program.

The authority is also pushing for $5.4 billion to install C.B.T.C. on another 75 miles of subway lines in a $68 billion capital plan being considered by the State Legislature in Albany.

If the money does not come through, riders will notice it during their commutes, said Andrew Rein, president of the Citizens Budget Commission, a watchdog group, which supports the signal upgrades.

“Modern signals mean faster, more reliable commutes,” he said. “Failure to update our antiquated signals means slower trains, more delays and explaining to your boss why you are late, again.”