.NET Framework 4.6 or a later update is already installed on this computer

To develop for .NET 4.6 in Visual Studio 2013 you need to install the targetting pack for 4.6.

The .NET 4.6 you’ve got installed is enough to run the programs, but it is not enough for development.

So follow the advice of the dialog, download the targetting pack.

Note that what you said you tried to download and install, that wouldn’t, was the normal runtime, and as you already know you have this installed. If you select the download option in the dialog it should open the right website, otherwise you should just open this page here (courtesy of @HansPassant in a comment):

Microsoft .NET Framework 4.6.1 Developer Pack and Language Packs for Windows 7 SP1, Windows 8, Windows 8.1, Windows 10, Windows Server 2008 R2 SP1, Windows Server 2012 and Windows Server 2012 R2

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