Air carrier Captain reported there are two L1 taxiway markings to the gate area in EWR.

Narrative

We flew flight XXX ZZZ-EWR and landed at XA:XX (night time); VMC. We read the airport information for EWR carefully since neither of us have been to EWR since the opening of the new A terminal. After landing we taxied to gate via K; S; A; RC; L1 and hold short of F3. Once inside the ramp area and on L1; my First Officer and I had a difficult time discerning where L1 would meet F3 for us to hold short of. I slowly continued to taxi on L1 while cross checking the Electronic Flight Bag (EFB). A few feet past the L1 taxi line continues around in a slight right turn toward the red shaded area where the old terminal is located. I then stopped the aircraft because we could see we had taxied off L1 according to our EFB and where our aircraft was on the moving map. Then ramp told us to stop since they could see we were not where we should have been on L1. We told them that we were on a line that said L1 but couldn't see F3. Ramp conceded that there are 2 L1 lines and they haven't removed the 'old' or unusable L1 line from the ramp area. They have painted new L1 lines but it is very hard to see and confusing for crews to note the difference. We were never close to anything that would have been an issue for contact with our aircraft. Once the airplane that was in front of our gate taxied out we then were cleared to taxi to our gate via taxi line A9. Crews need to be aware that old painted lines have not been removed and it is very difficult to understand the taxiway direction unless you've been there before. I recommend more information being sent out to crews or they immediately remove the old painted taxiway lines! We stopped once we realized we couldn't continue on L1 to get to F3 and we were in the red ramp area.