NPK Recovery will use women's urine, as it only manufactures women's urinals, although men's urine can also be used for the same purpose.
The process to convert the urine into liquid fertiliser is similar to treating waste water.
Bacteria is added to the urine which breaks it down into the ammonium nitrate that plants need to grow.
NPK Recovery said it hoped its plan would help to reduce the carbon footprint of the popular marathon.
Its founder, Hannah Vandenbergh, said: "Urine doesn't have to be a waste product and we're excited to be playing a small part in helping support the sustainability commitments of the iconic TCS London Marathon."
Kate Chapman, head of sustainability at London Marathon Events, said: "Part of our environmental strategy is to try and find an 'onward use' for all waste that is generated at our events, for instance composting, reusing, upcycling and much more besides.
"We are delighted that the urine from the urinals can be used for something so positive rather than going to waste."
NPK Recovery said if last year's 53,700 London Marathon finishers' urine had been captured, it could have made enough fertiliser for wheat to be turned into 3,142 loaves of bread.