How can I file an employer issued 1099misc for a bonus to avoid self employment tax as I am not self employed

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Your employer is reporting the bonus incorrectly. All payments from an employer to an employee should be treated as wages and included in the employee's W-2. It doesn't matter whether it's regular pay or a bonus. However, there is a way to report the bonus correctly on your tax return, in spite of your employer's error.

I assume that your employer reported the bonus in box 7 of the Form 1099-MISC, and that you also received a Form W-2 for 2016 from the same employer.

Follow the steps below to enter the 1099-MISC in TurboTax. The bonus will be included in the total wages on Form 1040 line 7. On the dotted line to the left of the amount on line 7 there will be a notation "F8919" and the amount. Form 8919 will be included in the return, with reason code H in column (c). Form 8919 will calculate the Social Security and Medicare taxes that your employer should have withheld from the bonus. The total of these taxes will appear on Form 1040 line 58 and will be included in your total tax liability.

• Click the Federal Taxes tab. (In TurboTax Self-Employed or Home & Business click the Personal Tab.)
• Click Wages & Income. (In TurboTax Self-Employed or Home & Business click Personal Income.)
• Click "I'll choose what I work on" or "Jump to a full list."
• On the screen "Your 2016 Income Summary," scroll all the way down to the last section "Less Common Income." Click the Start button for the last topic, "Miscellaneous Income, 1099-A, 1099-C."
• On the next screen click the Start button for "Other income not already reported on a Form W-2 or Form 1099."
• The next screen asks "Did you receive any other wages?" Select Yes and click Continue.
• The next two screens ask about household employee wages and sick or disability pay. Click Continue on these two screens without entering anything.
• The next screen asks "Did you earn any other wages? Select Yes and click Continue.
• The next screen asks the source of the other earned income. Select "Employee compensation that was not reported on a W-2." Ignore the note that says not to enter compensation for which you will receive a 1099. Click Continue.
• On the next screen, "Employee Compensation Not Reported on a W-2," click Continue.
• If you are filing a joint return, you will get a screen asking which one of you the income is for. Select your name and click Continue.
• On the next screen, "Report Your Wage Income," enter the employer's name and EIN from your W-2. When entering the EIN, you must enter the hyphen after the first two digits. For Total Wages Received, enter the amount on the 1099-MISC. Select Reason Code H. Click Continue.
• On the next screen, "Report as Wages," click Done.
• This returns you to the Miscellaneous Income screen. Click Continue.
  
  

Bonuses should be reported on a  W-2 form. Ask your employer to do so, and to void the 1099-MISC.

As SweetieJean pointed out, the first step is to ask the employer to correct things.

If the employer refuses, then you need to fill out Form 8919 to pay your half of the Social Security and Medicare taxes, then the IRS will tell your employer to correct it.
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What if your employer toke taxes out of your bonus and still gave you a 1099 can he do that ?

Is the income in box 3 or box 7 of the 1099MISC?  @phatkat123

Box 7 so that means he put me as a contractor right and he didn't even put that he toke taxes out in box 4 . 

You need to file the income reported to you as self-employment and pay the self-employment taxes.

See How do I enter a 1099 MISC from my current employer if I don't actually own/run my own business? It was for my intro period when I was hired but paid as contracted labor  for more information on your situation.

The employer toke taxes out of that ,that I was paid 

You stated that ‘the employer took taxes out of that’.  Are Federal withholding taxes reported in box 4 of the 1099-Misc?

Have you asked the employer to report the income on a corrected W-2 and void the 1099-MISC?

You can complete form 8919 to pay your half of the Social Security and Medicare taxes.  See here.

I'm very curious about this...because this happens almost every year with me. I receive a $1,000 bonus from my employer. I'm in Sales...and all it is, is a bonus for meeting my goal. These days I have to pay Self Employment tax with is crazy. 

Below you mentioned "I assume that your employer reported the bonus in box 7 of the Form 1099-MISC, and that you also received a Form W-2 for 2016 from the same employer." In this case the bonus is reported in Box 3. Now what?

Any help would be super appreciated. 

How can I claim 1099 misc for bonus $1000 ? 

What box is the income reported in?  and please review the answer from Champ rjs above as it explains how to handle the reporting if you received a 1099 with a bonus amount in Box 7 from your employer who also gave you a W-2.     @henryly1935

Hi, can I use the same described method to report bonus that wasn’t reported on W-2? My former employer didn’t pay taxes for the end of the year bonus. I got only w-2 and I see it only includes regular wages. No 1099 forms were received 

@winsirius You can enter wage income not reported on a W-2 form in TurboTax by following these steps:

1. Income and expenses
2. Less Common Income
3. Miscellaneous Income, 1099-A, 1099-C
4. Other income not already reported on a form W-2 or form 1099