[5][6] Since the 2010s, due to the heavily utilised infrastructure of the Pakenham line, significant improvements and upgrades have been made.

[11] In 1885, a number of level crossing removal works occurred between Flinders Street station and South Yarra due to an increase in freight and passenger operations.

[12] In 1915, the line between South Yarra and Caulfield was quadrupled, as part of level crossing removal works.

[14][15] The electrification of the line allowed for the introduction of Swing Door electric multiple unit trains for the first time.

[17] Previously, the stations between Dandenong and Pakenham were only served by regional passenger trains connecting Gippsland to Melbourne.

[18] In 1981, Pakenham line services commenced operations through the City Loop, after previously terminating at Flinders or Spencer Street stations.

[19] The commencement of operations involved the service stopping at three new stations—Parliament, Melbourne Central (formally Museum), and Flagstaff.

[20] The Loop follows La Trobe and Spring Streets along the northern and eastern edges of the Hoddle Grid.

[24] In 2018, the Pakenham East Depot opened for the newly acquired High Capacity Metro Trains.

[31] This outer portion of the line is one of Melbourne's main growth corridors, where farmland is being replaced with housing and commercial developments, leading to a rise in patronage.

[33][34] From 2025, services will cease to stop at Flinders Street, Southern Cross, Flagstaff, Melbourne Central, Parliament, Richmond and South Yarra stations due to the opening of the Metro Tunnel.

From March-June 2024, Narre Warren and Pakenham stations were elevated as part of Level Crossing Removal Project.

[40] Train services on the Pakenham line are also subjected to maintenance and renewal works, usually on selected Fridays and Saturdays.

The Pakenham line uses a fleet of electric multiple unit (EMU) High Capacity Metro Trains operating in a seven-car configuration, with three doors per side on each carriage and can accommodate of up to 1,380 passengers in each train-set.

Shared with the Cranbourne, Sunbury, and Airport lines, the rolling stock will consist of 70 High Capacity Metro Trains (HCMT), once fully delivered.

[49]Previously, the Pakenham line was served by a fleet of Comeng and Siemens Nexas trains.

[50] In comparison, the Siemens Nexas trains have not been retired, instead being moved onto other lines to replace older Comeng sets.

Since the end of 2022, the Pakenham line is almost exclusively operated by High Capacity Metro Trains.

This depot was built in 2018 to exclusively house and maintain 30 brand new High Capacity Metro Trains while they are out of service.

[53] Built by evolution rail the 118 hectares (290 acres) depot consists of a stabbling yard and an advanced driver training simulator.

[54][55] The depot is one of the most sustainable train maintenance regimes in Australia with:[55] Since the mid to late 20th century, the Pakenham line has used a fixed block three position signalling system designed for lower frequencies and less services.

These works valued at $1 billion includes the roll-out of 55 kilometres (34 mi) of HCS and communications systems on the aforementioned lines, allowing an increase in reliability and frequency.

[57] The line will be equipped with Bombardier’s CityFlo 650 communications-based train control system, that will enable operation at 2–3 minute headways.

[60] Host stations on the line also have customer service centres, however these are only staffed for a few hours during the morning peak.

[61] At the service centres, passengers can:[60] In compliance with the Disability Discrimination Act of 1992, all stations that are new-built or rebuilt are fully accessible and comply with these guidelines.

Leaving the existing Pakenham line alignment before South Yarra station, new stations will be built at Anzac, Town Hall (with connections to Flinders Street), State Library (with connections to Melbourne Central), Parkville, and Arden, before continuing onto the Sunbury line.

There have been two petitions [77][78]to the Victorian Government to halt the closure of Progress Street in Dandenong, where local businesses have argued there are safety and congestion concerns,[79][80][81] These projects will leave the entirety of the Pakenham line level crossing free by 2025, with projects on the Sunbury line leaving the entire Sunshine-Dandenong corridor crossing free by the opening of the Metro Tunnel in 2025.