Confucius' teachings were later turned into an elaborate set of rules and practices by his numerous disciples and followers, who organized his teachings into the Analects. Confucius' disciples and his only grandson, Zisi, continued his philosophical school after his death. These efforts spread Confucian ideals to students who then became officials in many of the royal courts in China, thereby giving Confucianism the first wide-scale test of its dogma.

Two of Confucius' most famous later followers emphasized radically different aspects of his teachings. In the centuries after his death, Mencius (孟子) and Xun Zi (荀子) both composed important teachings elaborating in different ways on the fundamental ideas associated with Confucius. Mencius (4th century BC) articulated the innate goodness in human beings as a source of the ethical intuitions that guide people towards rén, yì, and lǐ, while Xun Zi (3rd century BC) underscored the realistic and materialistic aspects of Confucian thought, stressing that morality was inculcated in society through tradition and in individuals through training. In time, their writings, together with the Analects and other core texts came to constitute the philosophical corpus of Confucianism.

This realignment in Confucian thought was parallel to the development of Legalism, which saw filial piety as self-interest and not a useful tool for a ruler to create an effective state. A disagreement between these two political philosophies came to a head in 223 BC when the Qin state conquered all of China. Li Si, Prime Minister of the Qin Dynastyconvinced Qin Shi Huang to abandon the Confucians' recommendation of awarding fiefs akin to the Zhou Dynasty before them which he saw as being against to the Legalist idea of centralizing the state around the ruler. When the Confucian advisers pressed their point, Li Si had many Confucian scholars killed and their books burned—considered a huge blow to the philosophy and Chinese scholarship.

Under the succeeding Han Dynasty and Tang dynasty, Confucian ideas gained even more widespread prominence. Under Wudi, the works of Confucius were made the official imperial philosophy and required reading for civil service examinations in 140 BC which was continued nearly unbroken until the end of the 19th century. As Moism lost support by the time of the Han, the main philosophical contenders were Legalism, which Confucian thought somewhat absorbed, the teachings of Laozi, whose focus on more spiritual ideas kept it from direct conflict with Confucianism, and the new Buddhist religion, which gained acceptance during the Southern and Northern Dynasties era. Both Confucian ideas and Confucian-trained officials were relied upon in the Ming Dynasty and even the Yuan Dynasty, although Kublai Khan distrusted handing over provincial control to them.

During the Song dynasty, the scholar Zhu Xi (AD 1130–1200) added ideas from Daoism and Buddhism into Confucianism. In his life, Zhu Xi was largely ignored, but not long after his death his ideas became the new orthodox view of what Confucian texts actually meant. Modern historians view Zhu Xi as having created something rather different, and call his way of thinking Neo-Confucianism. Neo-Confucianism held sway in China, Japan, Korea and Vietnam until the 19th century.

The works of Confucius were translated into European languages through the agency of Jesuit scholars stationed in China. Matteo Riccistarted to report on the thoughts of Confucius, and father Prospero Intorcetta published the life and works of Confucius into Latin in 1687.  It is thought that such works had considerable importance on European thinkers of the period, particularly among the Deists and other philosophical groups of the Enlightenment who were interested by the integration of the system of morality of Confucius into Western civilization.

In the modern era Confucian movements, such as New Confucianism, still exist but during the Cultural Revolution, Confucianism was frequently attacked by leading figures in the Communist Party of China. This was partially a continuation of the condemnations of Confucianism by intellectuals and activists in the early 20th century as a cause of the ethnocentric close-mindedness and refusal of the Qing Dynasty to modernize that led to the tragedies that befell China in the 19th century.

Confucius' works are studied by scholars in many other Asian countries, particularly those in the Chinese cultural sphere, such as Korea, Japan and Vietnam. Many of those countries still hold the traditional memorial ceremony every year.

The Ahmadiyya Muslim Community believes Confucius was a Divine Prophet of God, as were Lao-Tzu and other eminent Chinese personages.

In modern times, Asteroid 7853, "Confucius", was named after the Chinese thinker.