The City Council accepted SANDAG funds that cover the $1.55 million construction cost of the section of trail from Oceanside Boulevard to Wisconsin Avenue on Nov. 5.
The stretch of trail was put in, in April 2014 as the final link through Oceanside.
An earlier memo of understanding with SANDAG promised repayment in May 2013.
Gary Kellison, city senior civil engineer, said the reimbursement grant is standard, and a matter of procedure. The project was funded through SANDAG Transportation Enhancement Funds and Transnet Sales Tax.
The Coastal Rail Trail continues southbound to San Diego. The Oceanside section also connects to the eastbound San Luis Rey River Trail.