I think we need more details to understand what is going wrong for you.

Exactly what did you download and where from?

This is the main download page for SQLite:

https://www.sqlite.org/download.html

On that page is a section titled "Precompiled Binaries for Mac OS X (x86)”. 
Under that is a single link to the current version of the bundle of precompiled 
Mac tools: https://www.sqlite.org/2016/sqlite-tools-osx-x86-3130000.zip

If that isn’t what you are trying to run, you’ll need to explain what you 
downloaded.

Assuming it was that file:

After expanding the zip file you should have a folder containing three files: 
sqldiff, sqlite3, and sqlite3_analyzer.

These are command line tools which would normally be run from a shell inside 
Terminal.app. If you try to run one from Finder (by double clicking the icon) 
on a recent version of OS X, you should get a warning from Gatekeeper that they 
can’t be opened because they are from an unidentified developer (not a problem 
if they are launched from the shell). If you get past the Gatekeeper warning 
using one of the standard methods, Terminal should be launched, open a new 
window, and run the program. (That’s what happens for me.)

The warning about a damaged file is an odd one to get for command line tools, 
because it usually appears when an application’s digital signature doesn’t 
match the application bundle (indicating the application was modified). The 
SQLite command line tools are not digitally signed, which suggests Gatekeeper 
is getting confused somehow.

I’ve seen mention of cases where this message can appear for documents as well 
as applications, e.g. the following case where someone was using a third party 
file system driver via OSX Fuse - all downloaded files (with the 
com.apple.quarantine extended attribute) produced that message if 
double-clicked when the file was on the unusual file system, but were OK if 
subsequently moved to a normal HFS+ volume.

http://apple.stackexchange.com/questions/129966/files-wrongly-considered-as-damaged-in-encfs-volume

> On 9/07/2016, at 1:19 AM, Alex Fender <[email protected]> wrote:
> 
> I tried with Chrome and Firefox. I am using the default unzip tool in Mac.
> I double click the zip folder and then it unpacks a new folder to my
> desktop. When I open that folder, I then see the Sqlite programs. I double
> click to open and it says damaged.
> 
> On Fri, Jul 8, 2016 at 7:52 AM, Simon Slavin <[email protected]> wrote:
> 
>> 
>> On 8 Jul 2016, at 1:20pm, Alex Fender <[email protected]> wrote:
>> 
>>> After I download and unzip. I click and open Sqlite3 by double clicking.
>>> When I open the file, it says damaged and move to the trash.
>> 
>> Works fine on my Mac.
>> 
>> Which web browser are you using to download ?
>> Which program is used when you unzip the file ?

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