There is mention of Sarah's mother - in the University chapter during the various conversations between Joel and Ellie. Ellie asks Joel why he never went to University, and he says it is because he had Sarah at a very young age. I believe it went along the lines of "My childhood dream was to be a singer but I became a father early and it changed things."
Since Joel has custody of Sarah at the time of the outbreak, we can assume that the relationship dissolved for one reason or another. Joel seems to have a stable income, and it is possible he won custody in a legal battle. Maybe she was a drug addict or something, or maybe she had a baby really young and didn't end up wanting it, or maybe she died. A lot of possibilities that can stem from young people having an unexpected baby.
*edit*
"Sometime in his youth, Joel had a daughter named Sarah and was married to his wife for a short period of time. Saddled early in life with the responsibilities that come with being a father, he never had the opportunity to attend college. No mention is given as to the fate or whereabouts of Sarah's mother. However, it is revealed in a conversation between Joel and Ellie that the subject of whatever happened is very painful for Joel to talk about, and that he raised their daughter as a single parent for most of his life. "
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