The origins of the SSIEM may be traced to an informal meeting held in England at the Manchester Royal Infirmary in 1962 when an enthusiastic group of biochemists and paediatricians met to discuss phenylketonuria.

In May of the following year, the same group held a symposium in Sheffield which was entitled "Neurometabolic disorders in childhood". The Society was constituted formally in October 1963. The first symposium organised by the newly formed SSIEM was held in Liverpool in 1964 on the subject of "Biochemical approaches to mental handicap in children".

The history of the SSIEM is one of steady development. In 1967 the first corresponding members were appointed to provide communications with the wider membership. The first symposium to be held overseas was at Zurich in 1968.

Perhaps the most tangible achievement of the SSIEM has been its publication. Every one of its symposia has been published and this has provided invaluable review on specific topics in the field of inborn errors of metabolism. In 1978 the Journal of Inherited Metabolic Disease (JIMD) was launched. Membership now stands at over 1380 and is truly international with members from over 78 different countries.

In 2007, the Society established the Education and Training Advisory Committee to monitor the clinical training in paediatric metabolic medicine on behalf of the European Academy of Paediatrics and to organise the SSIEM Academy courses for paediatricians and laboratory scientists training in inherited metabolic medicine. The scientific component of the Academy course is organised in conjunction with ERNDIM.

In 2010, the Society established two special interest groups, for metabolic dieticians and for clinicians with an interest in IEMs presenting in adults. These special interest groups organise meetings within the annual Symposium and communicate information of interest. Membership of these groups is open to all members of the Society.