Mr Grayling met with leaders from the West Yorkshire Combined Authority in London yesterday to discuss the future of rail projects in the region.
It comes after the Transport Secretary was heavily criticised for failing to attend a backbench debate on transport in the North and sending a junior Minister on his behalf.
The council leaders, which include Bradford's Susan Hinchcliffe and Wakefield's Peter Box, released a statement describing the meeting with Mr Grayling as "challenging but positive and constructive meeting".
The Yorkshire Post understands that they asked for any decisions about the schedule of work for any rail electrification and the nature of consultations to be discussed with them first.
They said: "In the meeting he committed to ensuring that the Trans Pennine Rail Upgrade would be a significant share of government rail funding over the next five years, which we welcomed.
“We did stress though that we should be involved ahead of any final decisions being taken on the details of exactly what this would mean.
"We also stressed the importance of investment in the East Coast mainline, of HS2 East and the Calder Valley line plus Northern Powerhouse Rail with its stop in Bradford."
As Prime Minister and Chancellor respectively, David Cameron and George Osborne repeatedly pointed to their promise to electrify the trans-Pennine route as evidence of their commitment to the North.
Mr Grayling’s predecessor, Sir Patrick McLoughlin, commissioned a report identifying future lines which should be prioritised for electrification after 2019.
The Leeds-Harrogate-York and Calder Valley lines were among those recommended by the electrification task force’.
But earlier this year Mr Grayling cancelled electrification along a stretch of the Midland Mainline and suggested complete electrification may not be the answer to improving trans-Pennine journeys.
In September he announced £5m to help develop digital signalling as part of the upgrade to the trans-Pennine route which would allow more trains to use the track.