The Education Policy Institute (EPI) report found that Leeds Community Healthcare Trust had a median average waiting time of 117 days for children, from referral to start of treatment.
The EPI gathered data under the Freedom of Information Act from 62 mental health providers in England out of 64.
Analysts found that while median waiting times have fallen since 2015, children and young people in England waited an average of two months to begin treatment in 2018/19, double the Government's proposed four-week target.
But only three NHS trusts were found to have longer waiting times than Leeds Community Healthcare - West London Mental Health Trust (182 days), South Tyneside and Sunderland (129 days) and Alder Hey in Liverpool (124 days).
Leeds Community Healthcare Trust provides Child and Adolescent Mental Health Service (CAMHS) for children and young people under 18 and their families, and a new start-of-the-art CAMHS centre is due to open in Armley from September 2021.
Sam Prince, the trust's director of operations, said: "At Leeds Community Healthcare NHS Trust we see our emergency CAMHS referrals within four hours and urgent referrals within one week.
"The overall average for all routine first appointments in December 2019 was within target at 10.4 weeks.
"This is higher for routine autism and ADHD appointments due to significant increases in referrals.
"We are working hard to improve this and we are on track to do so by the end of the year.”
The report also found that, in England, one in four children and young people referred to specialist mental health services are rejected for treatment.
The EPI said it was unclear what support was available to the approximately 133,000 youngsters who were turned away, with the group including children and young people who have self-harmed, experienced abuse or have eating disorders.
Whitney Crenna-Jennings, senior researcher at the EPI and author of the report, said the system was "operating under great strain".
Denying children access to mental health treatment hinders academic performance and development, while mental ill-health is a barrier to social mobility, she added.
Emma Thomas, chief executive of mental health charity YoungMinds, said there could be "devastating consequences" if young people do not get support, including dropping out of school, self-harming or becoming suicidal.
An NHS spokesman said: "The NHS is actually ahead of its target on ensuring as many children as possible receive mental health care - seeing an extra 53,000 children, teenagers and young adults last year, a 14% increase on the year before and 22% more staff in services than five years ago, against a backdrop of rising referrals.
"It is a shame that the authors failed to check basic facts and policy commitments in this flawed analysis, including accurately reflecting how modern services for families operate in partnership with other agencies, and it is not the first time we have had to point out why the assumption that every referral should get NHS treatment when more appropriate support might be provided elsewhere - for example from schools and local authorities - is wrong."