
Known to all, iTunes is very picky about what kind of formats can be imported into it, and only a few of media formats are supported by iTunes, including MOV, M4V and MP4. Thus, you will certainly stumble if you try to import FLV files to iTunes for easy syncing with iDevices like iPad, iPhone. If you get used to the iTunes feature and want to add your FLV videos to iTunes, there is also a smart solution: converting FLV to iTunes friendly format first. The following paragraphs will bring you a step-by-step instruction on how to encode FLV to iTunes on Mac.
To convert FLV to iTunes on Mac (El Capitan, Yosemite and Mavericks), Brorsoft Video Converter for Mac would be the best choice. It is the ideal FLV to iTunes converter to help you encode FLV to iTunes compatible MOV/MP4/M4V video without compressing any video quality on Mac OS X. Besides FLV, it can also enables you to batch convert MKV, VOB, WMV, TiVo, MPG, AVI to iTunes video. Apart from that, people who want to make changes to the video can easily touch up the video with its built-in editor. For Windows users, you can convert FLV videos to iTunes with the help of Brorsoft Video Converter. Just download it and follow the steps below to get FLV files into iTunes.
How to Convert and add FLV files to iTunes on Mac OS X
Step 1. Import FLV videos
Install and run this FLV to iTunes Converter, add the FLV videos which you want to convert by directly dragging them to the main window of this program. Another way to import files can be done with clicking the Add button.

Step 2. Select iTunes supported format
Since iTunes supports MP4, M4V and MOV formats, you can click Format bar and choose any of the three from Common Video as the output file format. If you want to import .mkv to iTunes for playing on iPhone, iPad, iPod, Apple TV, etc., you can also directly select a format from decent device preset like iPad.

Step 3. Converting FLV to iTunes
When everything is OK, simply click the Convert button to begin the conversion from FLV to iTunes format. When the conversion is finished, you can import and play the convert flash FLV videos on iTunes or transfer them to iPhone, iPad via iTunes with ease.
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Source: Convert FLV to iTunes supported video format on Mac