You have not said whether this is biro or felt pen.
The following is our standard answer to ink removal problems for consumers or cleaners with no leather experience. Permanent markers are usually that and have redyed the leather so this will need recolouring as there is generally othing that will remove the dye without damaging the finish.
Removal will depend on what type of leather you have.
If the ink is on a pigmented leather then the first thing you should try is an ink stick.
http://www.lttsolutions.net/product.asp?product=6 The fresher the ink the more chance you have of removing it. Be sure to check the type of leather you have before doing this as if you use this on an aniline style it will not work and may leave a greasy mark which will not go away.
If an ink stick doesn't work a solvent based remover will need to be used and it may also remove finish and pigment so is best left to a technician.
Using hairspray/WD40 and all these other solvent cleaners is very risky as it can make the matter far worse as it can spread the ink over a bigger area and can sometimes then be impossible to fix.
Using alcohol, perfume, etc. can also be a little risky depending on how stable the finish is. If the finish is unstable this would remove pigment from the leather.
Nail varnish remover or any other solvents will also remove the finish and pigment which will need replacing.
DO NOT USE Baby wipes as they are about the worst thing you can use on a leather as they break down the finish and will eventually ruin it.
Please do not try milk or toothpaste these are silly ideas that will leave sticky residues on the surface which will help to break down the finish on your leather.
Magic erasers usually remove finish and pigment along with the ink. We have just tested these and they really do a lot of damage on leather. They act like a fine sandpaper and remove the finish.
Old ink will be harder to remove than new ink and may mean resorting to solvents which will also remove the finish. This is probably best left to a technician.
Silicones/furniture polish are the worst thing to use on leather as they will form a coating on the surface of the leather which will not allow any moisture to get to the leather and will eventually break all the finish down and make it crack.
Leather does not need conditioning it needs cleaning and protecting on a regular basis with water based products this will keep it rehydrated and supple. Oils will make things much worse.
Leather should be cleaned gently not scrubbed so 'elbow grease' will only do damage to the finish.
Hide food will not remove ink and will leave residues on the leather which will attract dirt and oils.
Using a good quality leather protector (one that works) will help make this problem easier should it happen again, it also does your leather good by protecting it against oils and dirt which ultimately make the pigment crack and the leather deteriorate.
If the ink is on an aniline leather then there is nothing that will work if leather cleaner has not. Basically you have redyed the leather and you would need a specialist to resolve the problem. Using a cleaner and protector on a regular basis will help to dissipate the ink and eventually it will not be so obvious.
If you need any help then just give me a ring on 01423 881027 and we will gladly talk you through