Afghan Allies Protection Amendments Act of 2018 This bill amends the Afghan Allies Protection Act of 2009 to authorize, in addition to any unused visas in prior fiscal years, up to 4,000 visas in FY2019 for the Afghan special immigrant visa program. That program provides special immigrant visa status for Afghans (and certain family members) who are threatened because of their work as translators, interpreters, or support staff for the U.S. government or its Armed Forces in Afghanistan. The bill also requires that the period of employment for Afghans eligible for the special visa end by December 31, 2021, and that Afghans seeking special immigrant status must apply to the Chief of Mission in Afghanistan by that same date.