Maternally derived amino acids (AA) are essential for early conceptus development, and specific transporters enhance histotrophic AA content during early ruminant pregnancy. In the present study we investigated AA transporter expression in early equine conceptuses and endometrium, during normal pregnancy and after induction of embryo–uterus asynchrony. ‘Normal’ conceptuses and endometrium were recovered on Days 7, 14, 21 and 28 after ovulation. To investigate asynchrony, Day 8 embryos were transferred to recipient mares on Day 8 or Day 3, and conceptuses were recovered 6 or 11 days later. Endometrial expression of AA transporters solute carrier family 38 member 2 (SLC38A2), solute carrier family 1 members 4 and 5 (SLC1A4 and SLC1A5) increased during early pregnancy, whereas solute carrier family 7 member 8 (SLC7A8), solute carrier family 43 member 2 (SLC43A2) and solute carrier family 7 member 1 (SLC7A1) SLC7A8, SLC43A2 and SLC7A1 expression decreased and the expression of solute carrier family 1 member 1(SLC1A1) and solute carrier family 7 member 2 (SLC7A2) was unaffected. In conceptus membranes, most transporters studied were upregulated, either after Day 14 (solute carrier family 7 member 5 – SLC7A5, SLC38A2, SLC1A4, SLC1A5 and SLC7A1) or Day 21 (SLC43A2 and SLC7A2). Asynchronous ET indicated that endometrial SLC1A5, SLC1A1 and SLC7A8 are primarily regulated by conceptus factors and/or longer exposure to progesterone. In conclusion, AA transporters are expressed in early equine conceptus membranes and endometrium in specific spatiotemporal patterns. Because conceptuses express a wider range of transporters than the endometrium, we speculate that the equine yolk sac has recruited AA transporters to ensure adequate nutrient provision during an unusually long preimplantation period.