The Children Chapel of Emmanuel Baptist church is an important ministry arm of the church that cares for children from one month old through twelve years. It is a vibrant arm of the church that caters for the proper spiritual, moral, academic and physical upbringing of children. This is done through many well organized programmes focused on the objectives of the children chapel. It is fascinating to know a brief about how the children chapel of the church started. The need to organize a separate worship service for the children was first seen by two women in the church, Mrs.C.A.Oluleye and Mrs R.B. Ayorinde. In 1977, they started by first organizing Sunday school lessons for the children when they saw that the children were not benefiting from the Adult Sunday School classes. Since there was no special provision for the children, they roamed about in the church premises during the Sunday school hour. Later, late Mrs. S.D.Iwaloye and late Mrs. F.B.Salako joined them.

The new church building was still under construction. The women saw the opportunity of utilizing the space in the new church building. They therefore led the children into the church building under construction for Bible lesson while regular adult oriented Sunday school lessons went on in the (now old) church building. After the Sunday school period, the children were led back into the church auditorium to join their parents and other adults in the main worship service.

Records of attendance taken for the Sunday worship service on 4th January, 1981 show that 519 children worshipped.

In 2012 the Wednesday prayer meeting was converted to Bible Club. The attendance at the first Bible club meeting was 98 Children and 10 Teachers.

In 1986 attendance varied from 600 to about 1,000 in the children's chapel. After the Sunday school the children went out of the worship service to play about in the spacious church premises. Factors responsible for this were, the children were not gaining from most adult- targeted worship service programmes and the (now old) church building being used had become too packed full for the children's comfort. The women led by Mrs.R.B.Ayorinde were quick to point out what they saw going on. They therefore proposed, and the Church Executive Committee agreed, that a separate worship service be conducted for the children in the new church building under construction.

The Women's Missionary Union of the church took up the responsibility of appointing their members from the various societies in turns to take part in conducting the children's worship service on Sundays. When the adults moved permanently into the new church building, they release the old auditorium to the children and regarded it as the children's chapel. Health professionals were called upon to check children that have health issues during the worship service, This later metamorphosed into the present day Emmanuel Baptist Church Clinic.

On 24th April, 1991, Mrs.R.B.Ayorinde and her group in the Children's Chapel introduced mid-week (Wednesday) evening prayer meeting for the children. Forty-one children and eleven teachers turned up for the first prayer meeting. In 2012 the Wednesday prayer meeting was converted to Bible Club. The attendance at the first Bible club meeting was 98 Children and 10 Teachers.

It is important to mention that with the introduction of the English Chapel, there was need to minister to the Children that came to the English Chapel. Mama Adeniyi and Dr.Akintunde took it upon themselves to gather the children to teach them the word of the God. In 2012 the Yoruba and the English children were mixed up together. Not quite long ago a new multipurpose hall was put in place for the children to make use of during their morning Sunday services.

In August 2013, the Children Department made my melody song book and Audio-CD for the sunbeam Band of the Nigerian Baptist Convention, which became the song book that is being used by all the Baptist Churches Sunbeam today. Today , the children department of the EMBC is waxing stronger and commited to raising godly children in our generation and beyond.