高速鐵路南港延伸段軌道工程範圍從臺北車站北端既有之軌道末端開始至南港車站末端結束，里程自（1K+000）至－（3K+583），屬南港軌道暨核心機電系統工程統包合約E201／E202標之一部分，由日商三菱東芝新幹線聯盟（MTSC）聯合承攬，上／下行線和月台區之軌道工程總長度12,395公尺，軌道型式以臺北至板橋隧道段既有之軌道為參考，採LVT（Low Vibration Track）型式之雙枕塊混凝土道床軌道鋪設，並於混凝土道床內增加斜向鋼筋加強穩固，同樣採JIS60斷面（Profile）連續長銲鋼軌、德製Vossloh扣件（W14 Type）。南港車站地下二層為高鐵/臺鐵共同車站大廳及穿堂層，地下一層為高鐵月台及軌道層，共設三島式月台，六股軌道。南港車站進站前設置雙橫渡線供列車於上／下行軌道轉換，共計8組BWG道岔（雙橫渡線道岔4組+進站道岔4組），道岔號數#16，固定岔心。
The HSR Nangang extension line construction starts from the north end of Taipei Main Station to the end of Nangang Station, in other words from (1K+000) to -(3K+583), and is a portion of the Nangang Rail and Core E&M System Contract E201/E202 signed with MTSC. The total rail length of the construction was 12,395 meters which included northbound/southbound and platform sections. This rail section adopted the rail type from Taipei Main Station to Banchiao Station which was low vibration track (LVT) with double-sleeper concrete bed. Tilted reinforced steel bar was added at the inner side of the roadbed to strengthen the rail. As the rail from Taipei to Banchiao, it used JIS60 profile consecutive long rod rails and Vossloh W14 type fastenings made in Germany. The second basement of Nangang Station is the joint station hall and concourse of HSR and TRA system and the first basement is the HSR platform and rail floor. The station comprised three island platforms and six stocks of rail. There is a double-crossover installed before the rail enters Nangang Station to convert of northbound/southbound trains there are a total of eight groups of BWG turnouts (four crossover turnouts and four entering turnouts), turnout #16 and a rigid crossing.