The history of religion in the Netherlands has been characterized by considerable diversity of religious thought and practice. From 1600 until the second half of the 20th century, the north and west had embraced the Protestant Reformation and were Calvinist. The southeast was predominately Catholic.see map Associated with immigration from Arab world (North Africa and the Middle east) of the 20th century, Muslims and other minority religions were concentrated in ethnic neighborhoods in the cities.

Since the 1960s, the Netherlands has become one of the most secular countries in the Western world. In a December 2014 survey by VU Amsterdam, more atheists (25%) were reported than theists (17%) for the first time in the history of the Netherlands. The majority of the remainder of the population identified as agnostic (31%) or ietsist (27%).

Prehistory and Early Middle Ages

Before the advent of Christianity, the Netherlands were populated by Celtic tribes in the South, which adhered to Celtic polytheism, and Germanic tribes in the North, which adhered to Germanic paganism. After the Roman Empire occupied the later southern Netherlands, Roman mythology became important there, as well as religions from the Middle East, including relics from Egyptian mythology, Judaism, Mithraism and later Christianity.

The oldest data on the profession of religion by the inhabitants of the regions that are now the "Netherlands" were passed down by the Romans. Contrary to what ancient sources seem to suggest, the Rhine, which clearly formed the boundary of the Roman Empire, did not form the boundary between residential areas of Celts and Germans. Germans settled south of it (Germani Cisrhenani), and many place names and archaeological finds indicate the presence of Celts north of the Rhine. Between these "Celtic – Germanic peoples" and later the Roman conquerors (romanization) a cultural exchange took place. An adaptation of polytheistic religions and other myths occurred among the various tribes, absorbing influences from Germanic, Celtic and later Roman mythology. Gods such as Nehalennia, Hludana and Sandraudiga are of Celtic or Celto-Germanic, origin; the Germanic people had such gods as Wodan, Donar and Frigg/Freya from Scandinavia. Jupiter, Minerva and Venus were introduced by the Romans. Tacitus described the creation myth of Mannus, a primitive man from which all Germanic tribes were said to have emerged. The Celts and Germans in the Low Countries were also most likely to have had tree shrines, following the example of the Old Norse Yggdrasil and the Saxon Irminsul and Donar's oak. Temples were probably built only during and after the romanization. Examples have been preserved in Empel and Elst.

From the 4th to the 6th century AD, the Great Migration took place, in which the small Celtic-Germanic-Roman tribes in the Low Countries were gradually supplanted by three major Germanic tribes: the Franks, the Frisians and Saxons. Around 500 the Franks, initially residing between the Rhine and the Somme, adopted Christianity, forced by their king Chlodovech. A large part of the area south of the Meuse River was controlled from the early Middle Ages to 1559 by Archdeacon of Kempenland, which was part of the Diocese of Tongeren-Maastricht-Liège. The see of this diocese, successively the cities of Tongeren, Maastricht and Liège, made up the base by which this part of the Netherlands was probably Christianized. According to tradition, the first Bishop of Maastricht, Servatius, was buried in this city in 384 CE. Only Bishop Domitianus (c. 535) is documented as having resided in Maastricht.

At the start of the 6th century, the first (Hiberno-Scottish) missionaries arrived. They were later replaced by Anglo-Saxon missionaries, who eventually succeeded in converting most of the inhabitants of the southern Netherlands to Christianity by the 8th century.

From the late 7th century, missionaries coming from England and Ireland, such as Boniface, Lebuinus, Ludger, Plechelm, Willehad and especially Willibrord, sought to convert the inhabitants of the areas north of the Meuse and Rhine rivers to Christianity. They had varying degrees of success, as attested by the (not always reliable) descriptions of their lives that have been written about them. While some sermons yielded success, Frisian king Radboud refused to be baptized by Wulfram. Because he was assured of getting to heaven if he repented and converted, Radboud instead chose an afterlife with his ancestors who, according to Wulfram, were in hell. After the Frisian–Frankish wars (c. 600–793) and the Saxon Wars (772–804), the Low Countries all fell under the rule of the Christian Frankish kings. They wanted their people to be both religious and political subjects, as the kings claimed divine right of leadership. The Old Saxon Baptismal Vow describes how one must renounce his old gods (described as "devils") and submit to the Christian Trinity.

In the 8th century, Anglo-Saxon missionaries such as Boniface continued efforts to Christianize the land inhabited by the Frisians. But Boniface was killed in 754 near Dokkum by the Frisians, because they thought he carried gold. The missionaries gradually succeeded in the conversion of the North in the 8th century. By the beginning of the 9th century, the Saxon-controlled northeastern regions were also subjugated and Christianized by Lebuinus, Plechelmus and Ludgerus. It took until 1000 CE before all pagan people were Christianized, and the Frisian and Saxon religions had died out. Elements of these religions were absorbed into the Christian religion, which is syncretic. During the following centuries, Catholic Christianity was the main religion in the Netherlands, but other practices likely survived in the conservative societies of the villages.

High and Late Middle Ages

Religious life was ubiquitous in medieval society. Important abbeys such Rolduc, Susteren, Sint Odiliënberg and Egmond were highly influential in the countryside. They were centers of learning and literacy. In the Christian centers of Utrecht and Maastricht, powerful chapters were established. From the 13th century, monastic and knightly orders settled in many cities, such as the Franciscans, Dominicans and knights of the Teutonic Order. They also took part in many of the 12th- and 13th-century crusades to the Holy Land (see Frisian participation in the Crusades).

Where justice until the 12th century existed largely in actions by kangaroo courts, which often administered trial by ordeal to establish a person's guilt or innocence, in the course of the 12th century, the ecclesiastical and secular powers took over more control of the justice system. The church rules (in particular by the Fourth Council of the Lateran in 1215) and the monarchs maintained the order. At the end of the Middle Ages, the Devotio Moderna (among others Geert Groote and Thomas à Kempis) created a spiritual innovation. In the 14th and 15th centuries, the first calls were heard for religious reform from within the Catholic Church. Geert Groote established the Brethren of the Common Life, an influential mystical order. The influence of humanism (particularly through the teachings of Erasmus and Dirck Coornhert) changed the Dutch world. It began to shift from a theocentric to an anthropocentric worldview.

Reformation in the Early Modern Period

Catholicism dominated Dutch religion until the early 16th century, when the Protestant Reformation began to develop. Lutheranism did not gain much support among the Dutch, but Calvinism, introduced two decades later, did. It began its spread in the Westhoek and the County of Flanders, where secret sermons in Dutch, called hagenpreken ("hedgerow orations"), were held outdoors. Gradually discontent among the Dutch grew, and erupted in 1566 with the so-called Beeldenstorm, a surge of iconoclasm. This quickly spread among all Dutch regions and finally resulted in what would become the Dutch revolt from Catholicism and Spanish control. During the Renaissance and the Protestant Reformation, an independent Dutch religious tradition began to take shape in the northern parts of the independent Netherlands.

The most prominent Dutch theologian was the humanist Desiderius Erasmus. He was critical of the abuses within the Catholic Church and called for reform, but he kept his distance from Martin Luther and Philip Melancthon. He continued to recognise the authority of the Pope. Erasmus emphasized a middle way, with a deep respect for traditional faith, piety and grace, and rejected Luther's emphasis on faith alone. Erasmus therefore remained a Catholic all his life. In relation to clerical abuses in the Church, Erasmus remained committed to reforming the Church from within. He also held to Catholic doctrines such as that of free will, which some Calvinist Reformers rejected in favour of the doctrine of predestination. His middle road approach disappointed and even angered scholars in both camps.Manfred Hoffmann, "Faith and Piety in Erasmus's Thought," Sixteenth Century Journal (1989) 20#2 pp 241–258

The 16th and 17th century were characterized by the Protestant Reformation, which greatly influenced the history of the Netherlands, especially in western and northern areas of the country. They also had influence with the eastern English shires, with which they were in contact through trading across the North Sea. The first wave of Reformation, initiated by Luther, did not come to the Netherlands.

The second wave of the Protestant Reformation, Anabaptism, became very popular in the counties of Holland and Friesland. Anabaptism was part of the Radical Reformation, a response to corruption both in the Catholic Church and in the expanding Magisterial Protestant movement. They refused to live the old way, and began new communities, which led to intense persecution. A prominent Dutch Anabaptist was Menno Simons, who initiated the Mennonite church. Another Anabaptist group attempted to take control of Amsterdam in 1535, in what is referred to as the Wederdopersoproer but was violently repressed and all participants killed. The action was inspired by the Annabaptist dominion of Münster one year earlier when Anabaptists, some from the Netherlands, took control of Münster. This action ended after a lengthy siege and the execution of the self proclaimed king Jantje van Leyden and other leaders. Anabaptists survived throughout the centuries and they were recognized by the States-General of the Netherlands in 1578. Institutionalized Dutch baptism was a model for both English and American Baptists.

The third wave of the Reformation, Calvinism, arrived in the Netherlands in the 1540s. Part of both the elite and commoners, mostly in Flanders, adopted this influence. Then in control of the Low Countries, the Spanish government, under Philip II started harsh persecution campaigns, supported by the Inquisition of the Catholic Church, as Protestantism was seen as threatening the royal government. In reaction to this persecution, the Calvinists rebelled. In the Beeldenstorm in 1566, they conducted iconoclasm, destroying statues, paintings, and other religious depictions and artifacts in churches. Also in 1566 William the Silent, Prince of Orange, a convert to Calvinism, started the Eighty Years' War to liberate the Calvinist Dutch from the Catholic Spaniards.