The Department for Education (DfE) said the money will help schools create an additional 740 school places for children with SEND as well as allowing schools to invest in facilities such as sensory rooms and playgrounds with specialist equipment.
The funding is in addition to £680m that has been pledged by the DfE to create 40,000 more good school places through expanding existing primary and secondary schools as well as building new schools in areas with increased demand for places.
The government said that the £50m to improve SEND facilities will see every council receive at least £115,000, with half of councils set to receive more than £225,000.
Children's minister Nadhim Zahawi said: "All parents want to send their child to a good local school, one that meets their individual needs and supports them to achieve their full potential, regardless of the challenges they may face.
"This funding will help to create thousands more school places across the country, with a clear focus on transforming the experience of education for children with SEND."
A spokesman for the National Network of Parent Carer Forums said it welcomed the increase in capital spending to increase places and improve facilities in schools for children with SEND.
"Specialist provision continues to be under great pressure across the country and it is vital this money makes the greatest impact," the spokesman said.
"We are pleased to note that local authorities will need to work with parents and carers to determine how it is most effectively spent."
The government said the funding announced today brought the total investment in new school places for children with additional needs to £265m, following the creation of a £215m fund last year.
Gail Walshe, head of parent carer participation at Contact, said schools had a duty to be accessible but their own experience had shown that was not always the case.
"Some schools lack capacity in their specialist units, or do not have a quiet room for children with sensory issues, or adequate changing facilities for children with personal care needs," she said.
"We hope that this top-up funding together with the £215m announced last year will help make a visible difference."
The DfE said the measures would build on the government's reforms to improve the lives of children and young people with additional needs through the introduction of education, health and care (EHC) plans.
Figures published this month by the DfE showed the number of children being refused SEN support following an assessment had more than tripled since EHC plans were brought in as part of the Children and Families Act 2014.
The percentage of children assessed by councils and denied an EHC plan rose from 3.76 (1,090 children) in 2015 to 6.73 (3,043 children) in 2017.
The DfE has said its overhaul of the assessment process for children with SEND in schools - the introduction of "pre-key stage standards" is expected in September - will ease the transition for children with additional needs onto the national curriculum.