Andrew Formica, chief executive at the group, said Brexit was immediately responsible for approximately 70% of retail outflows.
Post-referendum outflows were tempered by continued demand for UK Absolute Return and income strategies, specifically Strategic Bond.
Formica said: “We are very pleased with the supportive response we received from clients, employees and shareholders to the announcement of our merger with Janus Capital Group.
“Over the next few months, we will continue to serve our clients with our customary dedication, and use the time well to prepare for the launch of Janus Henderson Global Investors.”
Client sentiment was said tot remain “cautious”, in spite of a stronger economic backdrop than was expected.
A trading statement for Q3 reported a 6% increase in assets under management (AUM) from £95bn to £100.9bn during the period 1 July to 30 September, with currency gains through sterling weakness and positive markets behind the rise.
Beyond the UK business, Henderson reported a net outflow of £800m from its continental Europe and Latin American Sicavs as clients moved into cash in favour of European assets.
In the US mutual fund business, Global Equity Income gathered assets but European Focus suffered outflows, giving a net outflow figure of £300m.
Conversely, Henderson’s institutional business posted net inflows of £400m, with Formica confident over the “strong pipeline” of investment mandates expected in the fourth quarter.
Quarterly inflows comprised global technology, global natural resources, small and mid-cap US equities. In credit, flows in the pipeline look poised for emerging markets equity, global credit, European high yield, Australian fixed income and global buy-and-maintain credit.
Henderson said 77% of its funds outperformed their benchmarks over three years, which was consistent with the previous quarter.