Actually, Esperanto only bothers with gender when it's actually necessary. Inĝeniero can be of any gender one needs, or wants, it to be.
If, however, it becomes, for whatever reason, necessary to indicate that the engineer is female, then one has the option of saying inĝenierino. If I were to say: Mia edzino estas inĝeniero that is a fully correct statement. (Really, she is) But if one is looking at an Inĝenieramaso (a crowd of engineers) and wanted to specify that perky, mocha skinned, female engineer, with the stern expression (suddenly pointed right at me, "sorry!") then one can legitimately use inĝenierino, and then discuss the fallout with her.
I do hope that this helps.