The full project is funded through environmental clearance and final engineering. In late 2015, SANDAG completed an environmental assessment for the Federal Railroad Administration (FRA) under the National Environmental Policy Act (NEPA). The FRA is the lead agency for the environmental review. In January 2016, the FRA issued a Finding of No Significant Impact. In 2021, the project completed the federal lead transfer process from FRA to FTA and received FTA environmental clearance for construction. Phase 1 is anticipated to advertise for construction bids in late 2023, and construction is anticipated to start in the Spring of 2024.  Although not fully funded through construction, the full project is expected to be completed by 2030. 

Construction of Phase 1 is set to begin in late 2024 and include 0.8 miles of double-tracking north of the river, realigning the Stevens Creek channel. Phase 2 is not fully funded for construction and includes the double-tracked bridge, special events platform, realignment of the tracks south of Via de la Valley, double-tracking south of the river, and utility improvement.

The design phase of the full project was funded through 100% design and environmental with $8,581,320 in Transnet Funding and $6,704,698 in FRA - Passenger Rail Investment and Improvement Act (PRIIA) Funds. The FRA issued a Finding of No Significant Impact (FONSI) for the project in 2016. Environmental permitting was completed in October 2017 and the 60% design was completed in December 2017.

In July 2018, additional funding was secured to finalize design and prepare a Final Design package. Final Design funding consisted of $3.5 million in Senate Bill 1 - Local Program Partnership funding and $3.5 million in TransNet Funding. In January 2022, the project received $80,640 of SB 1, combined with the total of $5,081,320 of TransNet Funding. Final design for the full project was completed in February 2022. 

In 2021, funding was awarded to construct Phase 1 of the project and to prepare the Bid Ready package for advertise and award. Funding included a construction phase award of $30.5 million for a State Trade Corridor Enhance Program (TCEP) grant and a match of $25.8 million in FTA and FHWA Congestion Mitigation and Air Quality Improvement (CMAQ) funding provided through NCTD. NCTD is supporting the Phase 1 Bid Ready package with an FTA and CMAQ grant.

In April 2023, the Phase 2 Project received $100 million from the State of California Transit and Intercity Rail Capital Program (TIRCP) to complete the final design and partially funding of construction. SANDAG and NCTD are currently seeking construction funding in the amount of $230,752,744 for Phase 2.