Catalyzes the ATP-dependent transport of phospholipids such as phosphatidylcholine and phosphoglycerol from the cytoplasm into the lumen side of lamellar bodies, in turn participates in the lamellar bodies biogenesis and homeostasis of pulmonary surfactant (PubMed:16959783, PubMed:17574245, PubMed:27177387, PubMed:28887056, PubMed:31473345). Transports preferentially phosphatidylcholine containing short acyl chains (PubMed:27177387). In addition plays a role as an efflux transporter of miltefosine across macrophage membranes and free cholesterol (FC) through intralumenal vesicles by removing FC from the cell as a component of surfactant and protects cells from free cholesterol toxicity (PubMed:25817392, PubMed:26903515, PubMed:27177387). {ECO:0000269|PubMed:16959783, ECO:0000269|PubMed:17574245, ECO:0000269|PubMed:25817392, ECO:0000269|PubMed:26903515, ECO:0000269|PubMed:27177387, ECO:0000269|PubMed:28887056, ECO:0000269|PubMed:31473345}. This is the function of ABCA3 (ATP binding cassette subfamily A member 3, ENSG00000167972).