Neglected tropical diseases (NTDs) represent a serious problem in a number of countries around the world and especially in Africa and South America, affecting mostly the poor population which has limited access to the healthcare system. The drugs currently used for the treatment of NTDs are dated many decades ago and consequently, present in some cases very low efficacy, high toxicity and development of drug resistance. In the search for more efficient chemotherapeutic agents for NTDs, a large number of different compound classes have been synthesized and tested. Among them, ether phospholipids, with their prominent member miltefosine, are considered one of the most promising. This review summarizes the literature concerning the development of antiparasitic phospholipid derivatives, describing the efforts towards more efficient and less toxic analogues while providing an overview of the mechanism of action of this compound class against trypanosomatids. Phospholipid analogues are already known for their antiprotozoal activity. Several studies have been conducted in order to synthesize novel derivatives with the aim to improve current treatments such as miltefosine, with promising results. Photolabeling and fluorescent alkyl phospholipid analogues have contributed to the clarification of the mode of action of this drug family.