You do not specify the linguistic context. The following answer is based on the assumption that you mean the Old Norse dwarf name ‘Kíli’ (which is also the name of one of the dwarves depicted by J.R.R. Tolkien as living in Middle-earth). Note that the spelling is then Kíli, not Kili.
Based on the prevailing hypothesis regarding the origin of the name ‘Kíli’, the most logical female version would be ‘Keila’. Based on another hypothesis, however, it would be ‘Kilja’. Both keila and kilja exist as common nouns in Modern Icelandic, and both with several meanings (including ‘cone’, a species of fish and ‘bowling’ for keila and ‘(book in) paperback edition’ for kilja) and would seem very unusual as given names (but so too would Kíli).
In the context of Old Norse or Icelandic, both the form and the spelling of ‘Cilli’ and ‘Cilie’ exclude these as possible female versions of ‘Kíli’.