Otherwise, trains operate hourly in both directions seven days a week between either Unionville or Mount Joy stations and Union, with a small number of trips covering the full line to Old Elm.

Stouffville line trains operate non-stop through the shared segment, bypassing Scarborough and Danforth stations.

Only two years later, the Grand Trunk Railway leased most of the lines in the area as part of a major expansion plan and then purchased them outright in 1893.

On December 13, 2007, the government of Ontario announced funding to Metrolinx for network expansion, which included $20 million to build a second track to enable all-day two-way service between Union Station and Markham.

Lincolnville (now Old Elm) GO Station was built directly over GO Transit's Stouffville Yard, and so it consists of six tracks and platforms instead of the usual one or two.

On February 2, 2015, select trains began stopping at Danforth GO Station as part of a year-long pilot project to increase GO service within the City of Toronto.

Trains began operating from as early as 5 a.m. to as late as 11:45 p.m. with hourly service in both directions between Unionville and Union Station during the midday and evening.

[9] On August 31, 2019, GO Transit began providing bidirectional late-evening service between Union Station and Mount Joy, hourly between 9:30 p.m. and 11:30 p.m.

The final northbound trip continues past Mount Joy and arrives at Lincolnville at 12:29 a.m.[10] Starting on November 2, 2019, hourly two-way weekend train service between Mount Joy and Union Station began, with some morning and late night trips arriving in Lincolnville.

During midday non-peak hours, five southbound and five northbound trips are provided between Union Station and Mount Joy.

[11] Bus service is provided approximately every 30 minutes in the direction opposite that of the train trips during peak hours.

An additional southbound train operates out of Old Elm each morning but only provides service between Mount Joy and Union Station.

Southbound morning peak service, consisting of eight train trips, is provided under a frequency level of every 30–60 minutes, starting from a 5:20 a.m. departure from Old Elm.

Northbound evening peak service, consisting of five train trips, is provided under the same frequency level starting from a 3:14 p.m. departure from Union Station.

[17] After the implementation of a mandatory staff vaccination policy led to staffing shortages, and in response to the highly contagious Omicron variant, service across the GO system was once again reduced starting on January 10, 2022.

Near the Kennedy GO Station area are several industrial spurs serviced during the overnight hours by the Canadian National Railway, the former Uxbridge Sub owner.

Past Denison Street, the Stouffville train descends below 14th Avenue and the CN York Subdivision tracks before making its way back up, going beneath Highway 407 and stopping at Unionville GO Station.

As the train departs from Mount Joy GO station, the scenery becomes much more rural as the line continues north, crossing 19th Avenue, exiting Markham, and entering the Town of Whitchurch-Stouffville.

As of September 2023, on regular service days (excluding weekends and holidays), the first southbound train departs Old Elm at 5:14 a.m.

Weekend service was cut in early 2023, but resumed with 11 daily trips in each direction in September 2023 As of December 23, 2021, the entire length of the GO Transit Stouffville line (except for one crossing at the Markham/Stouffville border,[24] three crossings in the Town of Whitchurch-Stouffville,[25] and one crossing in the City of Toronto[26]) has train anti-whistling procedures implemented as the result of public outcry regarding the level of noise to which some residents were introduced as a result of the provision of increased rail service along the line.

The railroad authority Metrolinx worked closely with these cities to implement whistle cessation as quickly as possible provided that all safety requirements are met.

[31] In June 2013, GO Transit held a first "Public Information Centre" of an environmental assessment study for expanding rail service in the Stouffville Corridor.

[36] In February 2020, Metrolinx hosted a series of Public Information Centres detailing planned expansion and future service levels.

A less important but still noteworthy benefit is that grade separation is the only solution that effectively removes the need for train whistling without compromising public safety.

[41] There is also another crossing in Toronto that is included in this project that will be closed instead of grade separated since it runs through the middle of a residential neighborhood and underpass or overpass construction is infeasible.