Just use well protected ion cores or spinners.
Anyone else feel that rail guns are OP / the Meta
This thread shouldnt be in ‘Introductions’, perhaps move it to ‘Ship Building’
LawsonGage Layered shields and armor can stop pretty much everything, but the high cost of long railguns should make those enemy ships rather weak in other aspects, so I don't think they're as powerful as you find them. Before the accelerator nerv it was somewhat viable to fit as much railgun on your ship as you could after finishing everything else, but nowadays accelerators are hardly worth it when fighting against armored opponents (the penetration is still useful when going against ultralights or ships without internal protection, even tho you're probably better off buying some LCs for that money).
If you really need a dedicated long-rail counter for whatever reason, do as Lafiel said and get yourself a spinner or counter them with buried ion arrays.