Last week, the two politicians met to discuss ways of improving affordability and maximising the key benefits of the scheme.
Although London has shown it could pay for half the scheme, they have agreed on the need to ensure a funding package which works for both London and the rest of the country.
Mr Grayling said: “I am a supporter of Crossrail 2, but given its price tag, we have to ensure that we get this right.
“The mayor and I have agreed to work together on it over the coming months to develop plans that are as strong as possible, so that the public gets an affordable scheme that is fair to the UK taxpayer.
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Following the meeting, Mr Grayling said he was keen to launch a public consultation to help gather views to improve the scheme and clarify the position around the safeguarded route.
Mr Khan said: “Crossrail 2 is essential for the future prosperity of London and the South East, so I’m pleased that the transport secretary and I have reached an agreement to take this vital project forward.
“We will continue to work together to ensure the project is value for money and provides the maximum benefits for jobs and growth in the region over the coming decades.
“I look forward to moving to the next stage of consultation.”