Completion of the entire reproductive cycle, from the advent of pollination to the production of seeds with well-developed embryos, takes about 14 months. Pollination and the development of the sexual, or gametophytic, phase of the life cycle occur in the first year (April to September), but embryo development is not completed until the spring of the following year.

Ginkgo is dioecious, which means that pollen-producing structures and ovules are produced on separate trees. The reproductive structures are restricted to the spur branches, where they are evident in the spring in the axils of bud scales and foliage leaves.

The pollen-producing strobilus is a loose, pendulous, catkinlike structure consisting of a main axis to which are attached numerous appendages, each of which usually bears two microsporangia at its tip. Meiosis occurs in cells of the microsporangia, giving rise to numerous haploid microspores. Cell divisions take place within the microspores, resulting in the formation of five-celled pollen grains (male gametophytes).

Ovuliferous structures also arise in the axils of bud scales and the foliage leaves of spur branches. Each consists of a stalk that bears two or sometimes three or more erect ovules. An ovule is composed of an integument (the future seed coat) surrounding a tissue called the nucellus. It is in the nucellus that meiosis occurs, resulting in the formation of four haploid megaspore cells. It is at about this time that pollen grains are released from the microsporangia of male trees. The pollen (male gametophyte) is carried by wind currents and adheres to a pollination droplet, which exudes from the micropyle at the tip of the integument. Retraction of the droplet brings the pollen grains into a pollen chamber in the nucellus, where they develop into multibranched pollen tubes (male gametophytes).

One of the megaspores in the ovule that results from meiosis enlarges and undergoes a succession of free nuclear divisions (without wall formation). After about 8,000 haploid nuclei are produced, cell walls begin to form. After the female gametophyte becomes cellular, archegonia (normally two) are initiated at the surface toward the micropylar end of the ovule. An archegonium consists of neck cells and a large egg cell.

The basal end of the filament-like male gametophyte becomes suspended in a cavity above the female gametophyte (called the fertilization chamber). The spermatogenous cell of a male gametophyte divides, resulting in the production of two multiflagellated sperm. The sperm and the contents of the pollen tube are released into the fertilization chamber. The sperm swim in the liquid for a brief period of time. Approximately 1,000 flagella are attached to a spiral band at the anterior end. A sperm enters an archegonium and fuses with the egg nucleus. Ginkgo and the cycads are the only seed-producing plants that have motile sperm.

The growth of the embryo (embryogenesis) may begin shortly after fertilization but continues after the developing seeds fall to the ground. The embryo grows into the nutritive tissue of the female gametophyte. A seed at maturity consists of a dicotyledonous embryo, nutritive tissue of the female gametophyte, and the seed coat, which is made up of a hard inner layer and a fleshy, orange-coloured outer layer. Because of the presence of butyric acid, upon decay the fleshy layer emits an odour similar to rancid butter.