While Japan has a mixture of Shintō and Buddhist beliefs, funerals are almost always Buddhist ceremonies, and 91% of the funerals are Buddhist style. After death, the deceased's lips are moistened with water, in a ceremony called "Water of the last moment" (末期の水, Matsugo-no-mizu?). The household shrine is closed and covered with a white paper, to keep out the impure spirits of the dead. This is called Kamidana-fuji. A small table decorated with flowers, incense, and a candle is placed next to the deceased's bed. A knife may be put on the chest of the deceased to drive away evil spirits.

The relatives and the authorities are informed and a death certificate is issued. Organization of the funeral is usually the responsibility of the eldest son. A temple is contacted to schedule a funeral. It is believed by some that certain days are better for a funeral than others. For example, some days are known as tomobiki, literally "friend pulling", which is great for weddings, but to be avoided for funerals, as nobody wants to follow a dead person into the grave. The body is washed and the orifices are blocked with cotton or gauze. The last clothes are usually a suit for males and a kimono for females. A kimono for men is also sometimes used, but is less common. Make-up may also be applied to improve the appearance of the body. The body is put on dry ice in a casket, and a white kimono, sandals, six coins for the crossing of the River of Three Crossings, and burnable items the deceased was fond of (for example, cigarettes and candy) are placed in the casket. The casket is then put on an altar for the wake. The body is placed with its head towards the north or, as a second choice, towards the west (particularly in Buddhism, the west representing the western realm of Amida Buddha).

While in former times white clothes were worn for funerals, nowadays all guests for the funeral wear black. Men wear a black suit with a white shirt and a black tie, and women wear either a black dress or a black kimono. The black is of a special pitch-black shade. If the deceased family was an adherent to Buddhism, a set of prayer beads called juzu (数珠?) may be carried by the guests. A guest will bring condolence money in a special black and silver decorated envelope. Depending on the relation to the deceased and the wealth of the guest, this may be of a value equivalent to between 3,000 and 30,000 yen. The guests are seated, with the next of kin closest to the front. The Buddhist priest will then chant a section from a sutra. The family members will each in turn offer incense three times to the incense urn in front of the deceased. At the same time, the assembled guests will, in turn, perform the same ritual at another location behind the family members' seats. The wake ends once the priest has completed the sutra. Each departing guest is given a gift, which has a value of about half or one quarter of the condolence money received from this guest. The closest relatives may stay and keep vigil with the deceased overnight in the same room.

The funeral is usually on the day after the wake. The procedure is similar to the wake, and incense is offered while a priest chants a sutra. The ceremony differs slightly as the deceased receives a new Buddhist name (kaimyō). This name supposedly prevents the return of the deceased if his name is called. The length and prestige of the name depends also on either the virtue of the person's lifespan, or more commonly, the size of the donation of the relatives to the temple, which may range from a cheap and free name to the most elaborate names for 1 million yen or more. The high prices charged by the temples are a controversial issue in Japan, especially since some temples put pressure on families to buy a more expensive name. The kanji for these kaimyō are usually very old and rarely used ones, and few people nowadays can read them. At the end of the funeral ceremony, the guests and family may place flowers in the casket around the deceased's head and shoulders before the casket is sealed and carried to the elaborately decorated hearse and transported to the crematorium. In some regions of Japan, the coffin is nailed shut by the mourners using a stone.

The coffin is placed on a tray in the crematorium. The family witnesses the sliding of the body into the cremation chamber. A cremation usually takes about two hours, and the family returns at a scheduled time when the cremation has been completed. According to the Yamaguchi Saijo Funeral Parlor and Crematorium in Sapporo, it takes about an hour and a half to cremate an adult body, 45 minutes for a child, 15 minutes for a stillborn baby.

The relatives pick the bones out of the ashes and transfer them to the urn using large chopsticks or metal picks, two relatives sometimes holding the same bone at the same time with their chopsticks (or, according to some sources, passing the bones from chopsticks to chopsticks). This is the only time in Japan when it is proper for two people to hold the same item at the same time with chopsticks. At all other times, holding anything with chopsticks by two people at the same time, or passing an item from chopsticks to chopsticks will remind all bystanders of the funeral of a close relative and is considered to be a major social faux pas. The bones of the feet are picked up first, and the bones of the head last. This is to ensure that the deceased is not upside down in the urn. The hyoid bone (a bone located in the neck) is the most significant bone to be put in the urn.

In some cases, the ashes may be divided between more than one urn, for example if part of the ashes are to go to a family grave, and another part to the temple, or even to a company grave or a burial in space. Many companies have company graves in the largest graveyard in Japan, Okuno-In on Mount Kōya, burial place of Kūkai (774 - 835). These graves are for former company employees and their relatives, and often have a gravestone related to the company business. For example, the coffee company UCC has a gravestone in the shape of a coffee cup, and a metal rocket sits on top of the gravesite of an aeronautics company.[citation needed]

Depending on the local custom the urn may stay at the family home for a number of days, or be taken directly to the graveyard.

A typical Japanese grave is usually a family grave (Japanese: 墓,haka) consisting of a stone monument, with a place for flowers, incense, and water in front of the monument and a chamber or crypt underneath for the ashes.

The date of the erection of the grave and the name of the person who purchased it may be engraved on the side of the monument. The names of the deceased are often but not always engraved on the front of the monument. When a married person dies before his or her spouse, the name of the spouse may also be engraved on the stone, with the letters painted red. After the death and the burial of the spouse the red ink is removed from the stone. This is usually done for financial reasons, as it is cheaper to engrave two names at the same time than to engrave the second name when the second spouse dies. It can also be seen as a sign that they are waiting to follow their spouse into the grave. However, this practice is less frequent nowadays. The names of the deceased may also be engraved on the left side, or on a separate stone in front of the grave. Often, the name is also written on a sotoba, a separate wooden board on a stand behind or next to the grave. These sotoba may be erected shortly after death, and new ones may be added at certain memorial services.