Can I file head of household although my ex-husband will claim our son as dependent this year?

Yes you can if the child lived with you.   Answer the interview that the child is your child (not you and your present spouse if filing jointly),  YES - you have a custody agreement, and YES - the other parent is claiming this year.

Your child will NOT be your dependent - he will be a non-dependent for EIC, Dependent Care & HOH only.

This is the special rule for Children of divorced or separated parents (or parents who live apart)

http://www.irs.gov/publications/p17/ch03.html#en_US_2013_publink1000170876

The absent parent can claim the dependent (child's exemption) and Child Tax credit.

You can see all the rules for HOH at this IRS link:

http://www.irs.gov/publications/p17/ch02.html#en_US_2013_publink1000170792

You might consider amending your 2011 tax return if it increases your refund.

Thank you so much!
How do I amend my 2011 tax return?

First, I would go back to the preparer that you paid to do it correctly.  If, in fact, you did qualify for HOH and they failed to ask you about it, they should do it for you (for free I would hope).  

 Otherwise you would need a copy of the tax return, the 2011 software and then enter the information exactly as it was filed, claiming single and generate a 1040 form exactly as it was filed.  Then, you could amend that to change to HOH so the amended 1040X contains the changes.

Thank you!

Thank you both for posting.  I have the same family situation and just received a CP87A.  It was my intent to file as HOH and not claim my daughter.

what if the noncustodial parent already filed taxes and said she had the child more than half of the year but really didn't? She got the EIC for my qualifying child so what will happen when I file and she has already taken this?  I am not too worried about it because I don't qualify for EIC anyway based on income but I am worried about the IRS paying her for the EIC and then taking it away.

@Taxphobia  - If two taxpayers claim the same credit and the first e-filed, then the 2nd e-file will reject and must be mail filed.  The IRS will send letters to both taxpayers (takes a year or more) to get the taxpayers information that supports their claim.  The IRS will make a determination as to which taxpayer can keep the refund and which must pay it back with interest and possible penalties.

A person cannot qualify more than one taxpayer to use the head of household filing status for the year.

@alayna - That is true, each person qualifying for HOH would need a different child.  However, that is not the subject of this question, which was "Can the custodial parent claim HOH and the non-custodial parent claim the child's exemption?" and the answer to that is - yes (as explained in the answer above).

Thanks!

What if both parents are unmarried living together?

@kodibear07 - When both parents live with the child and are unmarried, then only one parent can claim the child and all the benefits.   The child should not be on the other parents tax return at all.  You can choose which parent.   Usually the parent with the higher AGI will get the most benefit.   That parent might also qualify for HOH if the HOH requirements are met.