The Burlington Northern Santa Fe Railroad was granted limited trackage rights through San Antonio by the Union Pacific as part of a "competition" guarantee to the Surface Transportation Board in 1996. The UP was in the process of getting its "merger" with the Southern Pacific ratified. The BNSF was granted trackage rights along the old Missouri Pacific and Missouri Kansas Texas lines north of San Antonio and along the old Southern Pacific line running to the west of the city. The lines to Corpus Christi and Laredo were not included in the arrangement. This would have an after effect in 2002 as the city began its final negotiations with Toyota. Even though Toyota uses Union Pacific for over 70% of its rail shipping needs, the company did not want to be totally reliant on just one rail company at its new factory. Its planned location is near to the old San Antonio Uvalde & Gulf line to Corpus Christi. As this had become part of the Missouri Pacific as early as 1925 and the Union Pacific had merged with MOPAC in 1982, the Union Pacific saw no obligation to share this extremely lucrative business with anyone else. BNSF does have the right to serve companies within the San Antonio area but has yet to do so. For a while, a plan was floated that the city would pay for the construction of a spur line from the line the BNSF did have access to heading west. The cost was astronomical and just getting planning permission lone would have taken years, let alone acquiring the land from presumably reluctant owners. Diplomacy by screaming headlines in the local newspaper ensued and the UP reluctantly conceded trackage rights to BNSF on the line as far as the plant from San Antonio, but no further. In other words, not as far as the port of Corpus Christi.

BNSF continues to run its trains through San Antonio but still does not have any local customers. It was involved, by default, in two of the four rail accidents that occurred in San Antonio in 2004. In both cases one of its trains was struck by a Union Pacific train. It may become involved in the clamor for rerouting trains around the city if they are not servicing businesses with the city. As it stands, the Union Pacific is taking the full intensity of this demand but the BNSF may become involved as the full extent of the costs and difficulties becomes clearer.