The signs being retrofitted debuted five years ago as part of a $29 million MBTA investment to improve audio announcements and pair them with scrolling text, to comply with the Americans with Disabilities Act. The federal government reimbursed 80 percent of the cost.

“We can’t deliver everything our customers want in almost all measure due to our financial challenges,” Davey said. “But this is a low-cost way to significantly improve the customer experience.”

Like so much about the Massachusetts Bay Transportation Authority, the reason for Boston’s delay of the countdown signs amounts largely to age and finances. But the signs were also not a priority until recently, when the MBTA started paying more attention to providing useful information to customers even if the agency lacks the money for other needs.

But while some agencies have spent millions of dollars on countdown signs, the T developed its own on a shoestring budget, with a small team of tech-savvy employees toiling long hours and working in a bunker so secretive that even Davey was not brought to their warren until they were confident bugs had been worked out.

Although the T has been ahead of the pack in providing predictions online and through smartphone applications, it lags behind many other cities’ systems in telling customers in stations when the train is coming. The Metro in Washington has displayed predictions since 2000. New York began installing countdown signs in 2007 and continues to roll them out across its vast system, while Chicago started in 2009.

“Now, you won’t have to wait 15 minutes,” said Sandra Seals, 23, a Bostonian waiting for the Red Line. “You can decide if you want to go out and do something and then come back, and not miss your train.”

Tuesday at South Station, riders expressed particular approval for the mezzanine signs that will greet customers before they pay at fare gates.

“I’m ecstatic that we’re announcing this,” said Davey, a daily subway commuter. “This is one of those items that I think customers have been asking for, waiting for, and wondering why we couldn’t do it for so long.”

The arrival of the new technology will end the uncertainty associated with subway riding in Boston since its 19th century inception — the wondering, the fidgeting, the craning over the tracks to peer into the tunnel, state Secretary of Transportation Richard A. Davey said.

The arrival times, ticking down in one-minute increments, will appear on LED signs that have hung above platforms and in station lobbies since 2007 but that until now have displayed only the date, time, and announcements.

The MBTA will activate long-awaited countdown signs on Wednesday telling riders when the next trains will roll into South Station, the start of a pilot program that could be extended to all 51 Red, Orange, and Blue Line stations by the end of the year.

Though they look like they should display predicted times, the closest they have come until now are the “attention passengers, the next train . . . is now approaching” announcements that are triggered when a train hits a track signal about a minute away. Because the “ping” tone preceding that announcement is the same as the one before all announcements, customers often perk up in expectation of a train, only to be told not to smoke or litter.

Before developing the new system, the MBTA, which had once sued MIT students who exposed flaws in the CharlieCard system, opened its data to software developers. That soon yielded dozens of applications at no cost to the MBTA and little or no cost to riders.

Many of those apps are for the bus system, which draws predictions in part based on global positioning satellites. And the transit agency has already installed LED displays at many commuter rail stations and Silver Line bus stops in recent years. But the subway apps were not as accurate, partly a reflection of the subway’s antiquated signal system.

So the T took $790,000 that remained unspent from the earlier display project, using it to buy a more robust computer server and upgrade the audio and display software. Then, the agency set out to improve its own subway predictions and build and test a system that could talk to the existing signs and speakers across the subway system.

Initially, Joshua Robin, the T’s director of innovation, worked with two others from the T’s operations technology group, a band that widened to 15 interns and young staff members when they were ready to start testing this spring. Carving out space inside a fireproof equipment room beneath the T’s Operations Control Center, they set up signs and speakers along with a computer tied to South Station cameras, to verify that arriving trains matched their predictions.

They also visited every station to check all speakers and signs, down to the pixel. And they ventured out late, often after midnight, to test whether they could switch the old server to the new one and push out announcements to stations — though not yet predictions — at a time when it was safer to make mistakes. If the hours seemed crazy, the group was determined to succeed, identifying as T riders as much as employees.

“We know how it will make people feel,” Robin said, during a visit to the bunker. “When we turn on these signs, it will be like refurbishing every station for every customer.”

They planned to run predictions briefly late Tuesday, then go live midmorning Wednesday. If South Station succeeds, Park Street will be added later this month, then Downtown Crossing in September. They will be monitored for at least a month while features are added and adjusted, with other stations to follow in batches of three.

The Green Line will not have countdowns because it has only a rudimentary tracking system, Robin said.

At South Station the other day, riders waiting on the outbound side watched in dismay as an inbound train came and went. After a few minutes that seemed longer, a “ping” signaled the possible arrival of an outbound train, but the announcement soon revealed it to be a second inbound one. People sighed, checked their watches.

“It’s always that way,” a weathered-looking man said, watching that train head toward Alewife. For a last uncertain time at the station, they waited, and they wondered.

Globe correspondent Matt Woolbright contributed to this report. Eric Moskowitz can be reached at emoskowitz@globe.com.

© Copyright 2012 Globe Newspaper Company.