Background: Data on abortion procedures costs are scarce in low- and middle-income countries. In Mexico, the only known study was conducted more than a decade ago, with data from years before the abortion legislation. This study estimated the costs, from the health system’s perspective, of surgical and medical abortion methods commonly used by women who undergo first-trimester abortion in Mexico. Methods: Data were collected on staff time, salaries, medications, consumables, equipment, imaging, and lab studies, at 5 public general hospitals. A bottom-up micro-costing approach was used. Results: Surgical abortion costs were US$201 for manual vacuum aspiration and US$298 for sharp curettage. The cost of medical abortion with misoprostol was US$85. The use of cervical ripening increases the costs by up to 18%. Staff comprised up to 72% of total costs in surgical abortions. Hospitalization was the area where most of the spending occurred, due to the staff and post-surgical surveillance required. Conclusions: Our estimates reflect the costs of “real-life” implementation and highlight the impact on costs of the overuse of resources not routinely recommended by clinical guidelines, such as cervical ripening for surgical abortion. This information will help decision-makers to generate policies that contribute to more efficient use of resources.